Ampliseq Version 2.0.0 "Blue Copper Kangaroo"

nf-core/ampliseq version 2.0.0 "Blue Copper Kangaroo" - 2021-06-29

Summary of changes

• Re-wrote whole pipeline in nextflow DSL2 instead of DSL1
• Three types of input is now supported: data folder, sample sheet, ASV fasta file
• ASV generation is now performed by DADA2 in R instead of DADA2 in QIIME2
• More reference taxonomy databases are now supported out of the box (SILVA, UNITE, PR2, GTDB, RDP)
• More data types can be analysed (Illumina SE & PE, PacBio, IonTorrent)

Detailed changes

Added

• #229 - --single_end for single-ended Illumina data
• #229, #245, #267 - Taxonomic classification with DADA2
• #229 - --dada_ref_taxonomy for taxonomic classification with DADA2's assignTaxonomy and addSpecies functions
• #278 - --qiime_ref_taxonomy for taxonomic classification with QIIME2
• #239 - Support of RDP database for DADA2 classification
• #237 - Support of UNITE database for DADA2 classification
• #229 - --input may point (1) at a fasta file ending with .fasta/.fna/.fa that will be taxonomically classified, (2) at a samples sheet ending with .tsv that allows analysis of multiple sequencing runs by reading the optional column run, or (3) at a folder input
• #229 - --sample_inference, --concatenate_reads, --illumina_pe_its; please check the documentation for their function
• #275 - Read count summary
• #274 - --skip_qiime to prevent any steps that are executed with QIIME2
• #272 - --cut_its to cut ASV sequence to ITS region before performing taxonomic classification with DADA2
• #280 - Added support for IonTorrent data
• #283 - --cut_dada_ref_taxonomy allows extracting expected amplicons from DADA2 reference taxonomy database

Changed

• #254 - Updated CamelCase parameters to be lower_case_snake_case:
  • multipleSequencingRuns to multiple_sequencing_runs
  • minLen to min_len
  • maxLen to max_len
  • maxEE to max_ee
• #277 - Requires nextflow version >= 21.04.0

Fixed

• #273 - Template update for nf-core/tools version 1.14

Dependencies

• #272 - New dependency ITSx v1.1.3
• #229 - Updated from cutadapt v2.8 to v3.2
• #229 - Updated DADA2 from v1.10 to v1.18.0, now not using QIIME2 for ASV generation any more
• #229 - Updated QIIME2 to v2021.2

Removed

• #229 - --manifest is superseeded by --input that can now also handle a sample sheet file input (required extension: .tsv)
• #229 - --Q2imported and untilQ2import are removed because pausing at that point is not neccessary
• #229 - --split is no longer supported, therefore all sample IDs have to be unique
• #229 - --classifier_removeHash and --qiime_timezone became unnecessary
• #229 - --onlyDenoising is deprecated in favour of --skip_taxonomy (which does the exact same thing)
• --taxon_reference became unnecessary
• #229 - --reference_database and --dereplication are not supported any more. --qiime_ref_taxonomy allows now choosing a taxonomic reference

Ampliseq Version 1.2.0 "Teal Bronze Lion"

nf-core/ampliseq version 1.2.0 "Teal Bronze Lion" - 2021

Added

• #106 - Added support for PacBio data
• Added --taxon_reference to be able to support both 'silva' and 'unite'
• #157 - Added possibility to run double cutadapt steps, --double_primer
• #211 - Added quality filter option --maxEE

Fixed

• #182 - Fix input in case there are no underscores in sample IDs
• #186 - Update github actions
• #187 - Sample ids are in incorrect order in feature-table from PacBio data
• #201 - Template update for nf-core/tools version 1.12.1
• #147 - Split make_classifier in two different processes that can be allocated different resources
• #183 - Don't fetch taxonomy/create classifier when run with --skip_taxonomy
• #180 - MultiQC, cutadapt and fastQC now work with --multipleSequencingRuns

Dependencies

• Updated from cutadapt v2.6 to v2.8

Ampliseq Version 1.1.3

nf-core/ampliseq version 1.1.3 - 2020

Added

• #170 - Cite paper for initial release
• #111 - Added parameter for user specified manifest file
• #118 - Added social preview images
• #135 - Added --trunc_rmin to make sure that auto trunc cutoff retaines a certain fraction of reads

Fixed

• #172 - Template update for nf-core/tools v1.11
• #163 - Template update for nf-core/tools v1.10.2
• #136 - Pipeline fails with remote working directory
• #152 - Don't fetch taxonomy/create classifier when run with --onlyDenoising

Dependencies

• Updated from MultiQC v1.6 to v1.9

Deprecated

• --reads is replaced by --input due to nf-core/tools v1.10.2

Ampliseq Version 1.1.2

nf-core/ampliseq version 1.1.2 - 2019

• No further changes, except a bugfix for the timezone issue found by @marchoeppner
• Specification of '--qiime_timezone' might be required to run the analysis appropriately

Ampliseq Version 1.1.1

nf-core/ampliseq version 1.1.1 - 2019

Pipeline Updates

• Update from QIIME2 v2018.6 to v2019.10, including DADA2 v1.6 to DADA2 v1.10

Bugfixes

• #78 - All sequenced classified to the same species

Ampliseq Version 1.1.0 "Silver Lime Bee"

nf-core/ampliseq version 1.1.0 "Silver Lime Bee" - 2019

Pipeline updates

• #40 - Added support for data originating from multiple sequencing runs
• #53 - DADA2 report is always exported
• #49 - Allowed more filtering options
• #5 - Introduced check for existence of input files
• Extended parameter sanity check, including #15
• #61 - Improved documentation
• #62 - Utilize nf-core/configs centrally for this pipeline
• #63 - QIIME imports files by using a manifest, giving more freedom with input file names
• #84 - Add proper nf-core logo

Bug fixes

• #57 - Indicate exact regex for sequencing file names
• #60 - publish demux.qza when --untilQ2import

Ampliseq v1.0.0 "Olive Steel Panda"

Initial release of nfcore/ampliseq!

The pipeline is a bioinformatics analysis pipeline used for 16S rRNA amplicon sequencing data.

The workflow processes raw data from FastQ inputs (FastQC), trims primer sequences from the reads (Cutadapt), imports data into QIIME2, generates amplicon sequencing variants (ASV, DADA2), classifies features against the SILVA v132 database, excludes unwanted taxa, produces absolute and relative feature/taxa count tables and plots, plots alpha rarefaction curves, computes alpha and beta diversity indices and plots thereof, and finally calls differentially abundant taxa (ANCOM). See the output documentation for more details of the results.