nf-core/ampliseq

Folder containing paired-end demultiplexed FastQ files

Forward primer sequence

Reverse primer sequence

Path to metadata sheet, when missing most downstream analysis are skipped (barplots, PCoA plots, …).

If samples were sequenced in multiple sequencing runs

Path to tab-separated table with sample IDs and paths to sequencing files

DADA2 read filtering option

DADA2 read filtering option [PacBio only]

DADA2 read filtering option [PacBio only]

Cutadapt will retain untrimmed reads, choose only if input reads are not expected to contain primer sequences.

Cutadapt will be run twice to ensure removal of potential double primers

DADA2 read truncation value for forward strand, set this to 0 for no truncation

DADA2 read truncation value for reverse strand, set this to 0 for no truncation

If —trunclenf and —trunclenr are not set, these values will be automatically determined using this median quality score

Assures that values chosen with —trunc_qmin will retain a fraction of reads.

Path to taxonomic reference database, currently accepts a qiime compatible file Silva_132_release.zip or a UNITE fasta file

Specify which database to use for taxonomic assignment. Either ‘silva’ or ‘unite’ (default: ‘silva’).

Path to QIIME2 trained classifier file (typically *-classifier.qza)

Remove all hash signs from taxonomy strings, resolves a rare ValueError during classification (process classifier)

Comma separated list of unwanted taxa, to skip taxa filtering use “none”

Abundance filtering

Prevalence filtering

Comma separated list of metadata column headers for statistics.

If PacBio data. Use this option together with —manifest

If the sequencing data has PHRED 64 encoded quality scores, otherwise PHRED 33 is assumed

A string that will be used between the prepended run/folder name and the sample name. Only used with “—multipleSequencingRuns”.

Naming of sequencing files

The output directory where the results will be saved.

Email address for completion summary.

Needs to be specified to resolve a timezone error

Keep additional intermediate files, such as trimmed reads or various QIIME2 archives

Skip all steps after importing into QIIME2, used for visually choosing DADA2 parameter --trunclenf and --trunclenr

Path to imported reads (e.g. “demux.qza”)

Skip all steps after denoising, produce only sequences and abundance tables on ASV level

Skip FastQC

Skip alpha rarefaction

Skip producing barplot

Skip taxonomic classification

Skip producing any relative abundance tables

Skip alpha and beta diversity analysis

Skip differential abundance testing

Skip MultiQC reporting