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.