The nf-core framework for community-curated bioinformatics pipelines.

Published May 16, 2022 | Version 2.4.1

Software Open

nf-core/ampliseq version 2.4.0 - 2022-09-07 Summary of changes

Custom DADA2 reference taxonomy databases are now supported.
Illumina NovaSeq data can be correctly processed.
ASV length filter is available for stricter QC.
Species classification is now reported in columns "Species" using DADA2's assignTaxonomy function or "Species_exact" using DADA2's addSpecies function, the latter only assigns exact sequence matches.

Detailed changes Added

#456 - An optional ASV length filter can be activated using --min_len_asv <int> and/or --max_len_asv <int>.
#458 - Samplesheet, ASV fasta file, and/or metadata sheet is now exported into <results>/input/
#459 - MIDORI2 CO1 database with keys midori2-co1=gb250 and midori2-co1 for --dada_ref_taxonomy
#460 - Taxonomic ranks for DADA2 taxonomic classification can be now adjusted using --dada_assign_taxlevels <comma separated string>.
#461 - A custom DADA2 reference taxonomy database can now be used with --dada_ref_tax_custom and --dada_ref_tax_custom_sp, typically accompanied by --dada_assign_taxlevels.
#446,#467 - Binned quality scores from Illumina NovaSeq data can be now corrected with --illumina_novaseq.
#477 - QC plots of DADA2's plotQualityProfile are now also produced after preprocessing.
#478 - Added GTDB R07-RS207 DADA2 taxonomy reference databases

Changed

#444,#457,#463,#465,#466,#469 - Updated the documentation.
#445 - The minimum number of total bases to use for error rate learning by default is 1e8 (DADA2, learnErrors, nbases). Previously, samples were read in the provided order until enough reads were obtained (DADA2, learnErrors, randomize=FALSE). Now, samples are picked at random from those provided (DADA2, learnError, randomize=TRUE) and a seed is set.
#453 - Export a few more basic QIIME2 fragments (zipped files) that can be easily imported into the correct QIIME2 version for custom analysis.
#464 - Reported taxonomic classifications on species level based on DADA2's assignTaxonomy (approximations) is now listed in column "Species" while exact matches based on DADA2's addSpecies are now reported in column "Species_exact".

Fixed

#448 - Updated SBDI export scripts to include Unite species hypothesis information if available.
#451 - Pairwise statistics will be now performed on a subset of metadata columns specified with --metadata_category instead of ignoring that setting.
#451 - Replace busybox with Ubuntu base image for GCP support.
#455 - Stop with descriptive error when only one of --trunclenf and --trunclenr is given, earlier it was silently ignored.
#474 - Template update for nf-core/tools version 2.5.1
#475 - Report software versions for DADA2_TAXONOMY

Dependencies

Tool	Previous version	New version
PICRUSt2	2.4.2	2.5.0
MultiQC	1.12	1.13a

Notes

If you use `nf-core tools` in your work, please cite the `nf-core` publication

Name	Size	Download all
nf-core/ampliseq-2.4.0.zip md5:76be96a1835a10167183700502ff963d	3.5 MB	Preview Download

Citations

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