Release Notes

Release Version: Nephele 2.32.4
Release Tag: Nephele_2024_May_01

Additions

• N/A

Removals

• N/A

Changes

• DADA2, DADA2 ITS, mothur, PICRUSt2 pipelines produce self-contained visualization HTML files with embedded CSS and JavaScript.

Fixes

• N/A

Release Version: Nephele 2.32.3
Release Tag: Nephele_2024_Apr_25

Additions

• N/A

Removals

• N/A

Changes

• N/A

Fixes

• DiscoVir pipeline: Unchecking the AMG option now correctly does not run any of the steps for producing AMGs.
• DiscoVir pipeline: Updated container image to fix intermittent failure in liftoff for estimating gene abundances.
• Fixed an error that caused several pipelines to be unable to accept .fq and .fq.gz files.

Release Version: Nephele 2.32.2
Release Tag: Nephele_2024_Apr_23

Additions

• N/A

Removals

• N/A

Changes

• Pipelines produce outputs.json, which contains information about the outputs

Fixes

• N/A

Release Version: Nephele 2.32.1
Release Tag: Nephele_2024_Apr_12

Additions

• N/A

Removals

• N/A

Changes

• N/A

Fixes

• Mapping validation: Check if all columns containing File in their name have corresponding existing files

Release Version: Nephele 2.32.0
Release Tag: Nephele_2024_Apr_01

Additions

• New pipeline: DiscoVir

Removals

• N/A

Changes

• N/A

Fixes

• WGSA2 pipeline: typo in outputted biom file causing incompatibility with Downstream Analysis pipeline

Release Version: Nephele 2.31.2
Release Tag: Nephele_2024_Mar_12

Additions

• N/A

Removals

• N/A

Changes

• WGSA2 pipeline: Diversity plots layout improvement

Fixes

• N/A

Release Version: Nephele 2.31.1
Release Tag: Nephele_2024_Mar_01

Additions

• N/A

Removals

• Upload via FTP

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.31.0
Release Tag: Nephele_2024_Feb_15

Additions

• N/A

Removals

• N/A

Changes

• Internal system update: containerization of pipelines

Fixes

• N/A

Release Version: Nephele 2.30.0
Release Tag: Nephele_2024_Jan_16

Additions

• New pipeline: Nanopore quality check

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.29.5
Release Tag: Nephele_2023_Nov_30

Additions

• N/A

Removals

• N/A

Changes

• User interface changes in pipeline documentation and results page

Fixes

• N/A

Release Version: Nephele 2.29.4
Release Tag: Nephele_2023_Nov_28

Additions

• N/A

Removals

• N/A

Changes

• Internal system dependencies update

Fixes

• N/A

Release Version: Nephele 2.29.3
Release Tag: Nephele_2023_Nov_07

Additions

• WGSA2 pipeline: added workflow tutorial and citation

Removals

• N/A

Changes

• WGSA2 pipeline: renamed TEDreads file from TED.tar.gz to TED.tar
• updated description text for pipelines

Fixes

• N/A

Release Version: Nephele 2.29.2
Release Tag: Nephele_2023_Oct_23

Additions

• WGSA2 pipeline: added link to download TEDreads (Trimmed, Error-corrected & Decontaminated) fastq files on the result page

Removals

• N/A

Changes

• WGS BioBakery pipeline: increased infrastructure capabilities

Fixes

• N/A

Release Version: Nephele 2.29.1
Release Tag: Nephele_2023_Oct_16

Additions

• N/A

Removals

• N/A

Changes

• N/A

Fixes

• QC pipeline: .gz.gz in returned cutadapt files

Release Version: Nephele 2.29.0
Release Tag: Nephele_2023_Sep_15

Additions

• WGS bioBakery: added BIOM-formatted files for frequently-used HUMAnN outputs

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.28.2
Release Tag: Nephele_2023_Sep_6

Additions

• DADA2 ITS:
  • Added new reference database: UNITE general FASTA release for eukaryotes (v9.0)
  • Added quality profile plots to the results page

Removals

• N/A

Changes

• DADA2 ITS: Updated the default reference database update to latest UNITE general FASTA release for fungi (v9.0)

Fixes

• QC pipeline: fixed hanging issue caused by Cutadapt

Release Version: Nephele 2.28.1
Release Tag: Nephele_2023_Aug_10

Additions

• N/A

Removals

• N/A

Changes

• Indicated software used to creating phylogenetic trees in DADA2 pipeline results

Fixes

• N/A

Release Version: Nephele 2.28.0
Release Tag: Nephele_2023_Aug_09

Additions

• User options for DADA2 pipeline:
  • Minimum bootstrap value for rdp
  • Multiple species ID
  • Pseudo-pooling
• Results to DADA2 16S, DADA2 ITS and mothur pipelines:
  • OTU table summary
  • Sample summary statistics
  • Read counts by sample
• Quality profile result to DADA2 16S pipeline

Removals

• N/A

Changes

• Internal DADA2 pipeline performance improvements
• In DADA2 pipeline Construct phylogenetic trees using MAFFT v7.520 (2023/Mar/22) and FastTree

Fixes

• N/A

Release Version: Nephele 2.27.2
Release Tag: Nephele_2023_Aug_04

Additions

• N/A

Removals

• N/A

Changes

• Nephele no longer decompresses input .gz files

Fixes

• N/A

Release Version: Nephele 2.27.1
Release Tag: Nephele_2023_Jul_20

Additions

• N/A

Removals

• N/A

Changes

• Activated FASTQ files validation for DADA2 pipeline

Fixes

• N/A

Release Version: Nephele 2.27.0
Release Tag: Nephele_2023_Jul_19

Additions

• N/A

Removals

• N/A

Changes

• WGSA2 pipeline updates:
  • updated existing DBs for taxonomic and pathway classifications
  • added additional databases for decontamination and tax classification
  • improved detailed metrics such as normalized abundance scores per gene and gene homologues
  • added addition of taxIDs to all tax classifications
  • improved visualization plots
  • added additional data-wide summary tables
• Updated team members at Project Team

Fixes

• N/A

Release Version: Nephele 2.26.1
Release Tag: Nephele_2023_Jul_13

Additions

• N/A

Removals

• N/A

Changes

• Made top species result optional

Fixes

• N/A

Release Version: Nephele 2.26.0
Release Tag: Nephele_2023_Jul_13

Additions

• Added MetaPhlAn BIOM File result to WGS BioBakery pipeline
• Added top species result to DADA2, DADA2 ITS and mothur pipelines

Removals

• Remove large tables from DADA2, DADA2 ITS and mothur pipelines result pages to shorten loading times

Changes

• N/A

Fixes

• Slow loading results page for pipelines that processed large datasets

Release Version: Nephele 2.25.6
Release Tag: Nephele_2023_Jul_10

Additions

• Added an example DADA2 pipeline results page
• Added MicrobiomeDB magic link to the result page

Removals

• N/A

Changes

• UI changes in the results page

Fixes

• N/A

Release Version: Nephele 2.25.5
Release Tag: Nephele_2023_Jun_26

Additions

• N/A

Removals

• N/A

Changes

• Google Tag Manager update

Fixes

• N/A

Release Version: Nephele 2.25.4
Release Tag: Nephele_2023_Jun_13

Additions

• Added Species_heatmap.html result to DADA2 and DADA2 ITS pipelines result pages

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.25.3
Release Tag: Nephele_2023_Jun_12

Additions

• N/A

Removals

• N/A

Changes

• Made seq_heatmap.html result optional in DADA2 and DADA2 ITS pipelines

Fixes

• N/A

Release Version: Nephele 2.25.2
Release Tag: Nephele_2023_June_12

Additions

• Added a table of contents to the user guide and the details page of each pipeline
• Implemented a popup survey that appears after job submission

Removals

• N/A

Changes

• Restricted the use of the forward slash (/) character in the header of the mapping file

Fixes

• N/A

Release Version: Nephele 2.25.1
Release Tag: Nephele_2023_Jun_08

Additions

• N/A

Removals

• N/A

Changes

• User interface improvements in the pipeline results page

Fixes

• N/A

Release Version: Nephele 2.25.0
Release Tag: Nephele_2023_Jun_07

Additions

• Added pipeline results pages that allow viewing and downloading singular results

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.24.3
Release Tag: Nephele_2023_May_30

Additions

• N/A

Removals

• Removed dependency on rpy2 for the 16S visualizations

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.24.2
Release Tag: Nephele_2023_May_17

Additions

• Added more log messages to QIIME2 pipeline to help users better track job progress

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.24.1
Release Tag: Nephele_2023_May_01

Additions

• SARS-COV-2 pipeline - ARTICplus method: produced variant effect summary for each sample

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.24.0
Release Tag: Nephele_2023_April_27

Additions

• N/A

Removals

• Removed the possibility to add new files to job reruns for local data uploads

Changes

• When reruning a job, previous inputs are not transferred by a webserver, but by a worker after the job starts

Fixes

• Fixed "504 Gateway timeout error which occurred during large job reruns

Release Version: Nephele 2.23.4
Release Tag: Nephele_2023_March_28

Additions

• Added new primer files for SARS-COV-2 ARTIC method:
  • V5.0.0_400
  • V5.1.0_400
  • V5.2.0_400
  • V5.2.0_1200
  • V5.3.2_400

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.23.3
Release Tag: Nephele_2023_March_23

Additions

• N/A

Removals

• N/A

Changes

• Visual updates to user registration form

Fixes

• N/A

Release Version: Nephele 2.23.2
Release Tag: Nephele_2023_March_13

Additions

• N/A

Removals

• N/A

Changes

• N/A

Fixes

• WGS - BIOBAKERY pipeline by forcing it to use mpa_v30_CHOCOPhlAn_201901 database

Release Version: Nephele 2.23.1
Release Tag: Nephele_2023_March_03

Additions

• feature-table.tsv output to QIIME2 pipeline

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.23.0
Release Tag: Nephele_2023_February_24

Additions

• Input FASTQ file validation in DADA2 pipeline

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.22.1
Release Tag: Nephele_2023_February_17

Additions

• N/A

Removals

• N/A

Changes

• N/A

Fixes

• data endpoint

Release Version: Nephele 2.22.0
Release Tag: Nephele_2023_February_15

Additions

• Check for poorly aligned sequences and reverse complement them in PICRUSt2 pipeline

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.21.10
Release Tag: Nephele_2023_February_13

Additions

• N/A

Removals

• N/A

Changes

• Internal improvements related to dependency management

Fixes

• N/A

Release Version: Nephele 2.21.9
Release Tag: Nephele_2023_January_20

Additions

• N/A

Removals

• N/A

Changes

• Internal improvements related to job log processing

Fixes

• N/A

Release Version: Nephele 2.21.8
Release Tag: Nephele_2023_January_11

Additions

• N/A

Removals

• N/A

Changes

• N/A

Fixes

• Download log functionality

Release Version: Nephele 2.21.7
Release Tag: Nephele_2022_December_22

Additions

• N/A

Removals

• N/A

Changes

• N/A

Fixes

• WGSA2 pipeline: temporary files generated by samtools got overwritten

Release Version: Nephele 2.21.6
Release Tag: Nephele_2022_December_9

Additions

• EC2 instance performance metrics dashboard

Removals

• N/A

Changes

• Internal WGSA pipeline updates allowing processing larger datasets

Fixes

• N/A

Release Version: Nephele 2.21.5
Release Tag: Nephele_2022_October_06

Additions

• N/A

Removals

• Plotting step that causes DADA2 pipeline to stall

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.21.4
Release Tag: Nephele_2022_August_24

Additions

• N/A

Removals

• N/A

Changes

• N/A

Fixes

• QC pipeline: The Cutadapt MultiQC module broke

Release Version: Nephele 2.21.3
Release Tag: Nephele_2022_August_18

Additions

• N/A

Removals

• N/A

Changes

• N/A

Fixes

• Incompleted job due to large strack trace report

Release Version: Nephele 2.21.2
Release Tag: Nephele_2022_August_4

Additions

• N/A

Removals

• N/A

Changes

• Internal enhancements

Fixes

• N/A

Release Version: Nephele 2.21.1
Release Tag: Nephele_2022_July_19

Additions

• N/A

Removals

• N/A

Changes

• Raised Google Drive limit to 2000 files per submission job

Fixes

• N/A

Release Version: Nephele 2.21.0
Release Tag: Nephele_2022_July_11

Additions

• N/A

Removals

• N/A

Changes

• Quality Check (QC) pipeline updates:
  • Python 3.5.3 to 3.8.13
  • QIIME2 2018.6 to 2022.2
  • FastQC v0.11.7 to v0.11.9
  • Trimmomatic 0.38 to 0.39
  • MultiQC 1.8.dev0 to v1.12
• mothur pipeline updates:
  • Python 3.7.3 to 3.9.2
• DADA2/DADA2 ITS pipeline updates:
  • Python 3.6.12 to 3.8.13
  • QIIME2 2020.11 to 2022.2
• QIIME2 pipeline updates:
  • Python 3.6.12 to 3.8.13
  • QIIME2 2020.11 to 2022.2
• SARS-CoV-2 pipeline updates:
  • Improved reporting of variants by adjusting filter thresholds (for ARTICplus method)
  • Python 3.7.3 to 3.9.2
  • samtools 1.9 to 1.11
  • deeptools 3.5.0 to 3.5.1
  • bedtools 2.27.1 to 2.30.0
  • pysam 0.16.0.1 to 0.19.1
  • SnpEff 5.0 to 5.1
• Downstream Analysis pipeline updates:
  • Python 3.6.12 to 3.8.13
  • QIIME2 2020.11 to 2022.2
• PICRUSt2 pipeline updates:
  • Python 3.6.13 to 3.8.13
  • PICRUSt2 2.4.1 to 2.5.0
• WGSA2 pipeline: considered sample count into size of produced plots, in order to create legible pdfs even for jobs with higher number of samples
• Google Drive upload method: listed only root folders on the first listing page

Fixes

• N/A

Release Version: Nephele 2.20.2
Release Tag: Nephele_2022_June_13

Additions

• N/A

Removals

• N/A

Changes

• User Interface: combined pipelines parameters tabs into one page

Fixes

• N/A

Release Version: Nephele 2.20.1
Release Tag: Nephele_2022_June_02

Additions

• N/A

Removals

• N/A

Changes

• WGSA2 pipeline: biom file's taxonomic information is read correctly by the MicrobiomeDB

Fixes

• N/A

Release Version: Nephele 2.20.0
Release Tag: Nephele_2022_June_01

Additions

• N/A

Removals

• N/A

Changes

• EC2 worker machines storage: switched to instance store from Elastic File System (Amazon EFS)

Fixes

• N/A

Release Version: Nephele 2.19.5
Release Tag: Nephele_2022_May_31

Additions

• N/A

Removals

• N/A

Changes

• N/A

Fixes

• WGSA2 pipeline: more accurately determine which TAX to filter and which to keep to final merged_tables files

Release Version: Nephele 2.19.4
Release Tag: Nephele_2022_May_25

Additions

• Added pipeline's names into logfile.txt
• Added metadata from mapping file into WGSA2's biom output file

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.19.3
Release Tag: Nephele_2022_May_24

Additions

• N/A

Removals

• N/A

Changes

• N/A

Fixes

• Fixed links to test datasets

Release Version: Nephele 2.19.2
Release Tag: Nephele_2022_May_18

Additions

• Added a new reference database option to DADA2 16S pipeline: SILVA v138

Removals

• N/A

Changes

• N/A

Fixes

• Fixed the error that prevented users to sign up

Release Version: Nephele 2.19.1
Release Tag: Nephele_2022_April_25

Additions

• N/A

Removals

• N/A

Changes

• N/A

Fixes

• Increased request buffer size to alleviate intermittent 502 responses for some users

Release Version: Nephele 2.19.0
Release Tag: Nephele_2022_April_25

Additions

• N/A

Removals

• N/A

Changes

• Moved to a new infrastructure with enhanced automatic security scanning capabilities

Fixes

• N/A

Release Version: Nephele 2.18.0
Release Tag: Nephele_2022_March_03

Additions

• N/A

Removals

• N/A

Changes

• Replaced WGSA (version 1) with WGSA2 (version 2)

Fixes

• N/A

Release Version: Nephele 2.17.3
Release Tag: Nephele_2022_February_18

Additions

• SARS-CoV-2 tutorial page

Removals

• N/A

Changes

• N/A

Fixes

• Fixed issues with serving large log files (view_log and download_log endpoints)

Release Version: Nephele 2.17.2
Release Tag: Nephele_2022_February_09

Additions

• Two additional primer file options (ARTIC V4.1 and IDT Midnight 1200) for SARS-CoV-2 (ARTIC method) pipeline

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.17.1
Release Tag: Nephele_2022_February_04

Additions

• Three primer file options from New England Biolabs (NEB) VarSkip for SARS-CoV-2 (ARTIC method) pipeline

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.17.0
Release Tag: Nephele_2022_January_31

Additions

• Added MicrobiomeDB link to QIIME2 16S pipeline results page

Removals

• QIIME1 ITS pipeline

Changes

• N/A

Fixes

• Fixed the job creation and completion times in the table in the user workspace

Release Version: Nephele 2.16.2
Release Tag: Nephele_2022_January_19

Additions

• N/A

Removals

• QIIME1 16S (retired) submission page

Changes

• N/A

Fixes

• Fix truncated `logfile.txt` file in user results archive

Release Version: Nephele 2.16.1
Release Tag: Nephele_2022_January_13

Additions

• Added status field in view_log page

Removals

• N/A

Changes

• N/A

Fixes

• Improved job log delivery user experience in view_log page

Release Version: Nephele 2.16.0
Release Tag: Nephele_2022_January_03

Additions

• N/A

Removals

• QIIME1 16S pipeline

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.15.1
Release Tag: Nephele_2021_December_27

Additions

• Added a filter option to remove unwanted taxa in Downstream Analysis pipeline
• Added log download button in view_log page
• Added a link to the view_log page in the workspace table

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.15.0
Release Tag: Nephele_2021_December_10

Additions

• Added ARTIC method to SARS-CoV-2 pipeline

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.14.0
Release Tag: Nephele_2021_December_08

Additions

• Logs can be displayed even after job has finished processing (view_log endpoint)

Removals

• N/A

Changes

• Redesigned log viewing page (view_log endpoint)

Fixes

• Fixed multiple security vulnerabilities

Release Version: Nephele 2.13.1
Release Tag: Nephele_2021_November_30

Additions

• N/A

Removals

• N/A

Changes

• N/A

Fixes

• Fixed SyntaxError in Quality Check pipeline

Release Version: Nephele 2.13.0
Release Tag: Nephele_2021_November_29

Additions

• NEW Pipeline: DADA2 ITS

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.12.2
Release Tag: Nephele_2021_September_30

Additions

• N/A

Removals

• N/A

Changes

• biobakery pipeline version has been updated to 3.0.0.a.7 from 0.13.2. See the pipeline detail page

Fixes

• N/A

Release Version: Nephele 2.12.1
Release Tag: Nephele_2021_September_15

Additions

• N/A

Removals

• N/A

Changes

• mothur pipeline version has been updated to 1.46.1 from 1.40.5. See the pipeline detail page

Fixes

• N/A

Release Version: Nephele 2.12.0
Release Tag: Nephele_2021_August_30

Additions

• NEW Feature: My Workspace

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.11.3
Release Tag: Nephele_2021_August_19

Additions

• N/A

Removals

• N/A

Changes

• Allowed PICRUSt2 pipeline to accept both Paired-end and Single-end mapping file

Fixes

• Fixed the issue that caused DADA2 pipeline to hang at filterAndTrim step

Release Version: Nephele 2.11.2
Release Tag: Nephele_2021_August_16

Additions

• N/A

Removals

• N/A

Changes

• Updated Nephele 2 GitHub repository link

Fixes

• Fixed mapping file validation blinking error
• Fixed "invalid choice" bug while re-run QIIME 2 pipeline

Release Version: Nephele 2.11.1
Release Tag: Nephele_2021_August_10

Additions

• Added phylogenetic tree in the DADA2 amplicon pipeline
• Added stratified option in the PICRUSt2 pipeline

Removals

• N/A

Changes

• Upgraded DADA2 version from 1.10 to 1.18 for the DADA2 amplicon pipeline

Fixes

• N/A

Release Version: Nephele 2.11.0
Release Tag: Nephele_2021_July_29

Additions

• NEW Pipeline: Metagenome Inference: PICRUSt2
• NEW Reference Database for DADA2 pipeline: HOMD 15.22

Removals

• N/A

Changes

• N/A

Fixes

• Downstream Analysis Pipeline: re-run previous job with Upload New function failed to run

Release Version: Nephele 2.10.0
Release Tag: Nephele_2021_June_21

Additions

• NEW Pipeline: Whole Metagenome Sequence Assembly (WGSA)

Removals

• N/A

Changes

• New design for Analyze page (from Homepage)

Fixes

• N/A

Release Version: Nephele 2.9.0
Release Tag: Nephele_2021_May_27

Additions

• NEW Pipeline: QIIME2

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.8.2
Release Tag: Nephele_2021_Apr_30

Additions

• Downstream Analysis pipeline runs diversity core-metrics-phylogenetic step when a tree file (.nwk) is uploaded.

Removals

• N/A

Changes

• Downstream Analysis pipeline is now using QIIME 2 2020.11 version.
• Homepage layout update (v.2.8.1)

Fixes

• N/A

Release Version: Nephele 2.8.0
Release Tag: Nephele_2021_Apr_16

Additions

• NEW Pipeline: SARS-CoV-2 (beta) pipeline

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.7.0
Release Tag: Nephele_2021_Apr_02

Additions

• Implemented NIAID Globus Endpoint to upload sequence files. (please see how to use Globus for your job submissions).

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.6.0
Release Tag: Nephele_2021_Jan_21

Additions

• Enabled automatic transfer of a biom file (from DADA2, mothur and DA pipelines) to microbiomeDB.org (please see more details)

Removals

• N/A

Changes

• bioBakery pipeline version update from 0.3.1 to 0.13.2.
• Increased the file size can be uploaded via a browser from 1GB to 2GB per file.

Fixes

• Downstream Analysis (DA) pipeline parameter form error.
• Fixed on an issue with some files stay on Elastic File System (EFS) longer.

Release Version: Nephele 2.5.0
Release Tag: Nephele_2020_Nov_09

Additions

• Implemented Google Drive and Illumina BaseSpace to upload sequence files.

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.4.1
Release Tag: Nephele_2020_Sept_24

Additions

• N/A

Removals

• N/A

Changes

• Increased the file size can be uploaded via a browser from 450MB to 1GB per file.

Fixes

• N/A

Release Version: Nephele 2.4.0
Release Tag: Nephele_2020_Apr_15

Additions

• Increased the Nephele concurrent pipeline job submission capacity and added a queuing system to accommodate the high demand.

Removals

• N/A

Changes

• Improved Nephele's mothur pipeline error handling to prevent the non-responding status of the pipeline with large input files.

Fixes

• N/A

Release Version: Nephele 2.3.3
Release Tag: Nephele_2020_Jan_29

Additions

• Ion Torrent data processing (beta) feature is added in DADA2 pipeline. If you have Ion Torrent data for 16S, you can use the DADA2 pipeline.
• QIIME BIOM V2 file can be submitted in the Downstream Analysis pipeline.

Removals

• N/A

Changes

• N/A

Fixes

• Gateway timeout issue for job resubmission due to unzipping has been fixed

Release Version: Nephele 2.3.2
Release Tag: Nephele_2019_Dec_16

Additions

• reCAPTCHA has been added to the Sign-Up page

Removals

• N/A

Changes

• QIIME 1 pipeline is now running the core diversity without the taxonomy plots. For the taxonomy plots, we recommend using the Amplicon Downstream Analysis pipeline after the QIIME job is complete.

Fixes

• An issue with "I received an error email; now what?" accordion menu not opening has been fixed

Release Version: Nephele 2.3.1
Release Tag: Nephele_2019_Oct_08

Additions

• Alpha significance of Shannon diversity feature is added on Downstream Analysis (DA) pipeline.

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.3.0
Release Tag: Nephele_2019_Aug_21

Additions

• NEW Pipeline: Amplicon Downstream Analysis pipeline

Removals

• N/A

Changes

• Update QIIME pipeline instance with 64GB of memory (m5.4xlarge)
• Updated QIIME ITS OTU database from the version 7.1 (2016-11-20) to version 8.0 (2018-11-18)

Fixes

• N/A

Release Version: Nephele 2.2.8
Release Tag: Nephele_2019_Jun_13

Additions

• DADA2 pipeline updates
  • Greengenes for the OTU picking reference database
  • Option added in the DADA2 pipeline to allow for concatenation of paired-end reads instead of merging
  • Added DECIPHER as a taxonomic assignment method
• QIIME ITS pipeline
  • Closed Reference and De Novo for the OTU picking analysis type
  • A release identifier has been added in the logfile.txt

Removals

• N/A

Changes

• EC2 time has set to Eastern Standard Time (EST) Zone

Fixes

• N/A

Release Version: Nephele 2.2.7
Release Tag: Nephele_2019_May_29

Additions

• N/A

Removals

• N/A

Changes

• N/A

Fixes

• Fixed an issue to display the user's email address after signing in.

Release Version: Nephele 2.2.6
Release Tag: Nephele_2019_May_16

Additions

• Rarefied OTU table is included in DADA2 output

Removals

• Removed excessive intermediate files (join_pair folder) from QIIME pipelines

Changes

• Updated Boostrap version to 4.3.1

Fixes

• Fixed biom format when only one sample in dataset
• Fixed filtering out for low abundant organisms in a heatmap

Release Version: Nephele 2.2.5
Release Tag: Nephele_2019_Apr_01

Additions

• Updated MultiQC 1.6 to 1.8dev

Removals

• N/A

Changes

• Updated Bootstrap version from 3.3.7 to 4.0.0
• Updated the name of the SILVA database in the DADA2 forms to reflect the version of the database. NOTE: The database used has not changed, the name was updated in the form to more accurately reflect what is used.

Fixes

• N/A

Release Version: Nephele 2.2.4
Release Tag: Nephele_2019_Feb_14

Additions

• Updated DADA2 1.6 to 1.10

Removals

• N/A

Changes

• N/A

Fixes

• N/A

Release Version: Nephele 2.2.3
Release Tag: Nephele_2019_Feb_01

Additions

• Added Human Oral Microbiome Database (HOMD) in 16S pipelines

Removals

• N/A

Changes

• N/A

Fixes

• Modifications to code retrieving remote files via FTP
• Restored unnecessarily deleted intermediate files from the mothur pipeline result file

Release Version: Nephele 2.2.2
Release Tag: Nephele_2018_Nov_28

Additions

• Added Nephele Webinar (11.16.2018) on Tutorials page

Removals

• N/A

Changes

• Enable QIIME1 to run core diversity in parallel

Fixes

• Fixed minor infrastructure bug fix in the pipeline exception handling.

Release Version: Nephele 2.2.1
Release Tag: Nephele_2018_Nov_08

Additions

• Added Tutorials page

Removals

• N/A

Changes

• "Visualization tutorial" and "Importing into Phyloseq" moved to new Tutorials page

Fixes

• Issue with the mothur pipeline that stalls on the 'dist.seqs' step for large dataset has been resolved.
• Issue with slow data transfer using the FTP method has been resolved.

Release Version: Nephele 2.2.0
Release Tag: Nephele_2018_Oct_05

Additions

• NEW PIPELINE: Pre-processing Quality Check (QC)
• NEW PIPELINE: DADA2 Single End

Removals

• 18S "Coming Soon" button has been removed due to the lack of interest. Please email us if you would like to provide us your feedback on the 18S pipeline.

Changes

• Cleaned up unnecessary intermediate files from the mothur pipeline result file

Fixes

• Issue with the remove lineage option in mothur pipeline has been fixed.

Release Version: Nephele 2.1.2
Release Tag: Nephele_2018_Sep_13

Additions

• "Closed reference" option restored in 16S QIIME1 PE and SE pipelines

Removals

• N/A

Changes

• N/A

Fixes

• Issue with QIIME1 "Closed reference" OTU picking method has been fixed.

Release Version: Nephele 2.1.1
Release Tag: Nephele_2018_Sep_07

Additions

• N/A

Removals

• Temporary removal of "Closed reference" option in 16S QIIME1 PE and SE pipelines

Changes

• N/A

Fixes

• Issue with QIIME1 running the default OTU picking method regardless of the user selection has been fixed.

Release Version: Nephele 2.1.0
Release Tag: Nephele_2018_Aug_29

Additions

• mothur 1.40.5 pipeline
• Tutorial for importing Nephele results into Phyloseq

Removals

• Updated supported file extensions; removed support for legacy file formats

Changes

• Modify sampling depth calculation in 16S pipelines (see FAQ for more details)

Fixes

• Check the mapping file for non-ASCII characters to prevent errors during downstream analysis

Release Version: Nephele 2.0.2
Release Tag: Nephele_2018_Jul_27

Additions

• Added sampling depth option to QIIME1 pipeline for downstream analysis

Removals

• N/A

Changes

• N/A

Fixes

• Fixed a bug in the sampling depth calculation for QIIME1 and DADA2 that was introduced in version 2.0.1 which caused the sampling depth to be set too low for some datasets
• Corrected typos in mapping file instructions
• Corrected reference for Nephele in the about pages

Release Version: Nephele 2.0.1
Release Tag: Nephele_2018_Jul_19

Additions

• Added filter and trim parameters for the DADA2 Paired End pipeline (see pipeline detail page)

Removals

• N/A

Changes

• N/A

Fixes

• An issue that caused the PICRUSt step to not be correctly initiated in QIIME1 Single End has been fixed
• Corrected typos in mapping file instructions

Release Version: Nephele 2.0
Release Tag: Nephele_2018_July_02

Additions

• NEW PIPELINE: 16S DADA2 Paired-end FASTQ pipeline
• Added interactive mapping file validation
• Added a Sign-Up page and email validation which you'll need to complete prior to your first job submission
• Added a "resubmit a job with jobID" function
• Added 16S Data Visualization tutorial page
• Automated the result data expiration after 90 days of the job completion.

Removals

• Removed the promotional code request page and its functionality and replaced it with a sign-up
• Removed 16S QIIME SFF pipeline
• Removed 16S QIIME FASTA&QUAL pipeline
• Removed 16S QIIME Paired-end Multiplex pipeline
• Removed 16S mothur SFF pipeline
• Removed WGS bioBakery SFF pipeline
• Removed HMP Comparison feature
• Removed 3D microbiome page
• Removed the ability to change the instance type for a job

Changes

• Updated bioBakery WGS pipeline including visualization
• Updated 16S data visualization ampvis2 R package.
• Updated the job submission workflow to a step-by-step style wizard
• Updated file upload to allow a multi-file fastq files instead of a single zip file
• Updated the SILVA database to release 132
• Modified default instance type from c3.4xlarge to c5.4xlarge (the instance for DADA2 is m5.4xlarge, WGS bioBakery is m5.12xlarge)
• Modified mapping file templates remove unnecessary columns
• Updated UserGuide, FAQ page and About pages
• Modified Nephele homepage design
• Updated pipelines parameters and help text
• Re-wrote the site from the ground up using a new framework

Fixes

• N/A

Release Version: Nephele 1.8
Release Tag: Nephele_2017_Jun_30

Additions

• Introduced OpenMP-based parallelization to accelerate both mothur and QIIME 16S analysis pipelines
• Added a feature to automatically filter out rare OTUs (<0.05% abundance) in QIIME analyses

Removals

• None

Changes

• Upgraded mothur version from 1.38 to 1.39.5
• Updated the SILVA database to release 128
• Updated the UNITE/INSDC representative/reference sequences for the QIIME ITS pipeline to version 7.1 (2016-11-20)
• Updated FastTree to version 2.1 to support double precision and OpenMP (the support of double precision eliminates an issue associated with rounding errors on tree branches less than 0.0001, which were likely to produce trees that failed to accurately describe divergence among isolates)
• Replaced USEARCH with the open-source VSEARCH alternative, for both mothur- and QIIME-based 16S analysis pipelines
• Modified all pipelines using the SILVA reference database to align against SILVA NR rather than SEED database
• Updated references, including replacing downloadable citation files in EndNote, RIS, and BIB formats with an NCBI Collection URL

Fixes

• Fixed an issue in QIIME pipelines with a user-defined selection of SILVA for reference taxonomy selection being ignored and running with the default Greengenes-based taxonomy classification
• Corrected a bug that resulted in failure to remove chimeric sequences in QIIME-based pipelines
• Addressed an issue in mothur pipelines that prevented removal of low-abundant reads as specified in the "difference rank" parameter

Release Version: Nephele 1.7
Release Tag: Nephele_2016_Dec_22

Additions

• Implemented functional annotation analysis capability using PICRUSt in QIIME and mothur paired end pipelines (see help text in submission form for additional details)
• Added Shannon diversity analysis step to all 16S pipelines
• Developed better error capturing for improved troubleshooting, including reporting of NEPHELE_WARNING and NEPHELE_ERROR notifications in the log file (see FAQ for more details)
• Added species-level plotting for 16S analysis when using Greengenes reference database, by user request (note: we caveat this feature addition with typical warnings regarding reduced confidence in interpretation of results at this level of granularity)
• Added support for users of Box.com file storage/sharing service to submit files to Nephele from Box via URL (note: see FAQ for additional details)

Removals

• Removed "OTU_heatmap" directory from mothur paired end outputs, which is instead being created using phyloseq and can be found in "nephele_outputs" directory
• Removed selection of m3.2xlarge instance type

Changes

• Modified QIIME and mothur pipelines' usage of UCLUST algorithm, in favor of SortMeRNA for clustering when selecting open reference OTU picking
• Changed classification step in mothur paired end pipeline to use SILVA NR database instead of SEED database
• Updated processing of compare-to-HMP to use pre-computed BIOM files for faster processing
• Modified calculations for sequence filtering while running core diversity analysis in all 16s pipelines to use percentage of median OTUs rather than the maximum, including modifying the default fraction value for subsampling from 0.1 to 0.2
• Changed default max_length cutoff value in mothur from 300 to 450 base pairs
• Updated mothur paired end pipeline to stop processing and report in log file when mean joined sequence length is 100 base pairs or less
• Adapted email text and reply-to address for improved tracking for support and troubleshooting
• Modified color of phyloseq-generated heat maps from ice blue to the deep red found on the Nephele homepage
• Moved runtime.txt file from WorkFolder.zip to PipelineResults.zip for improved troubleshooting
• Updated relevant tutorial videos, pipeline diagrams, user guide details, and references section to reflect changes from this release

Fixes

• Addressed issue with slowing or termination of jobs during high-usage periods due to AWS-imposed limits
• Fixed issue with failed pipelines due to too many OTUs to plot by skipping plotting when plots would be too dense to create or interpret
• Corrected issue with spaces in name of URL-submitted files by automatically removing spaces
• Fixed false-positive validation error for sequence read directories having gzipped inputs
• Addressed compare-to-HMP job failures related to too few reads in HMP tissue sources

Release Version: Nephele 1.6
Release Tag: Nephele_2016_Oct_11

Additions

• Added .mapping file extension for mothur MiSeq pipelines
• Created Phyloseq-based visualizations, including heat maps, relative abundance stacked bar charts, and mini bar plots, for all QIIME and mothur amplicon jobs

Removals

• Removed bioBakery 16S pipeline due to maintainability challenges

Changes

• Modified Nephele homepage design
• Updated relevant tutorial videos, pipeline diagrams, user guide details, and references section to reflect Phyloseq visualization updates

Fixes

• Fixed issue with QIIME ITS pipeline not working

Release Version: Nephele 1.5
Release Tag: Nephele_2016_Aug_12

Additions

• N/A

Removals

• N/A

Changes

• Moved interface fields for comparing to Human Microbiome Project (HMP) data to separate section on second form screen for amplicon-based analyses
• Updated email confirmation message to more clearly indicate compare-to-HMP settings that were selected
• Modified all email address references to one that automatically logs to Nephele's tracking system

Fixes

• Addressed issue in mothur pipelines where HMP comparisons were run, even if not specified
• Fixed problem with large data file output not transferring to AWS S3 after pipeline completion

Release Version: Nephele 1.4
Release Tag: Nephele_2016_Jul_13

Additions

• NEW PIPELINE EXTENSION: Compare 16S analysis results using QIIME or mothur to the Human Microbiome Project (HMP) healthy human subjects cohort
• Added description of HMP comparison pipeline to User Guide
• Added FAQs page
• Updated Release Notes page

Removals

• N/A

Changes

• Modified form field to allow user the ability to select which reference database to use for 16S comparisons (e.g., Greengenes versus SILVA), in addition to the original selection of percent similarity threshold value.
• Set default value of 16S QIIME pipeline's reference database to SILVA_99 (from original Greengenes_99)

Fixes

• Addressed issue in file validation timeouts that occassionally resulted in 404 errors
• Fixed bug with QIIME FASTQ Single End pipeline failures resulting from extra metadata columns were added to the mapping file

Release Version: Nephele 1.3
Release Tag: Nephele_2016_Jun_13

Additions

• NEW PIPELINE: QIIME ITS analysis for paired end Illumina data
• Added option to turn off core microbiome analysis for QIIME pipelines
• Improved mapping file validation to ensure that TreatmentGroup column has a minimum of two distinct values, has only alphanumeric characters, and does not allow spaces
• Added CHIMERAS_FOUND.txt to nephele_outputs directory of QIIME pipeline results to indicate how many chimeras were found
• Added Release Notes page

Removals

• Disabled selection of diversity analysis and plots in mothur & QIIME pipelines; these are now run conditionally based on user inputs

Changes

• Refactored Mothur MiSeq pipeline to utilize SILVA SEED database v. 123
• Updated Mothur MiSeq pipeline to automatically skip beta diversity analysis if fewer than 3 samples are provided
• Modified mapping file validation error messages to make it clearer what actions to take if validation fails

Fixes

• Addressed issue with auto-detection of phred scores for Illumina 1.9 data
• Corrected pipeline failure issue when spaces exist in the name of any input file
• Fixed issue with empty html links for bar plots

Release Version: Nephele 1.2
Release Tag: Nephele_2016_Apr_28

Additions

• Released feature improvement for QIIME Single and Paired End pipelines to successfully process single, demultiplexed sample
• Created new mapping file templates for all pipelines
• Improved mapping file validation to catch SampleID containing non-alphanumeric or period characters, which causes pipelines to fail
• Created downloadable citations file in EndNote (.enw), Research Information Systems (.ris), and BibTeX (.bib), accessible from the References page
• Added "compute_core_microbiome" step to QIIME pipelines and updated associated pipeline diagrams
• Added Release Notes page

Removals

• N/A

Changes

• Modified generation of heatmaps at the Order taxonomic rank to improve readability of output images
• Updated mapping file templates for QIIME pipelines
• Set Nephele pipeline diagram URLs as relative URLs based on environment
• Modified help text to reflect QIIME maximum sample size update in "Additions" section above

Fixes

• Addressed issue with some analysis jobs not starting properly
• Fixed issue with calculation of zero OTU hits that had created a divide-by-zero error in "plot_taxa_summary" processing step
• Set processing of QIIME pipelines' "fraction of maximum sample size" parameter such that if 0 is provided in Nephele form (which causes pipeline failure), QIIME's default value is used instead
• Corrected QIIME core diversity depth calculation, which was previously incorrect
• Improved QIIME Single End pipeline to accept variable length barcodes
• Added versioning tag to HTML, CSS, and JavaScript to fix 404 errors related to system deployments

Release Version: Nephele 1.1
Release Tag: Nephele_2016_Mar_23

Additions

• Added capabilities to QIIME pipelines, including Shannon diversity analysis and the ability to perform core diversity analysis even when there are very few samples (e.g., due to trimming of reads at high thresholds)
• Created tutorial video on homepage and in User Guide for submitting sample files to Nephele, including sample files for testing
• Updated Nephele's mapping file validation feature to prevent submission of jobs that are likely to fail during processing
• Added more detailed references and citations for QIIME, mothur, and a5-miseq
• Implemented Google Analytics tracking
• Established new support tracking system and built hooks into Nephele code base

Removals

• N/A

Changes

• Changed version of QIIME from 1.8 to 1.9.1
• Modified default instance type from c3.8xlarge to c3.4xlarge
• Modified mapping file templates to work with mapping file validation improvements
• Restructured information in the User Guide regarding available pipelines and how they work
• Moved references from User Guide to About page

Fixes

• Resolved issue with pipelines failing when sequence files were submitted within multi-layered zip directories
• Fixed typo on homepage