nf-core/ampliseq

Either a tab-seperated sample sheet, a fasta file, or a folder containing zipped FastQ files

Forward primer sequence

Reverse primer sequence

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

If data is single-ended PacBio reads instead of Illumina

If data is single-ended IonTorrent reads instead of Illumina

If data is single-ended Illumina reads instead of paired-end

Part of ITS region to use for taxonomy assignment: “full”, “its1”, or “its2”

Cutoff for partial ITS sequences. Only full sequences by default.

If samples were sequenced in multiple sequencing runs

If analysing ITS amplicons or any other region with large length variability with Illumina paired end reads

Not recommended: When paired end reads are not sufficiently overlapping for merging.

Mode of sample inference: “independent”, “pooled” or “pseudo”

Comma separated list of metadata column headers for statistics.

Formula for QIIME2 ADONIS metadata feature importance test for beta diversity distances

Naming of sequencing files

If the functional potential of the bacterial community is predicted.

If data should be exported in SBDI (Swedish biodiversity infrastructure) Excel format.

Specifies the random seed.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Email address for completion summary.

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.

DADA2 read filtering option

DADA2 read filtering option

DADA2 read filtering option

Enable SSU filtering. Comma separated list of kingdoms in Barrnap.

Minimum taxonomy agglomeration level for DADA2 classification

Maximum taxonomy agglomeration level for DADA2 classification

Minimum taxonomy agglomeration level for QIIME2 classification

Maximum taxonomy agglomeration level for QIIME2 classification

Name of supported database, and optionally also version number

If the expected amplified sequences are extracted from the DADA2 reference taxonomy database

Name of supported database, and optionally also version number

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

Ignore input files considered too small (<1KB) for individual samples and continue the pipeline without those samples.

Ignore files considered too small (<1KB) after trimming and continue the pipeline without those samples.

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

Abundance filtering

Prevalence filtering

Skip FastQC

Skip primer trimming with cutadapt. This is not recommended! Use only in case primer sequences were removed before and the data does not contain any primer sequences.

Skip annotating SSU matches.

Skip all steps that are executed by QIIME2, including QIIME2 software download, taxonomy assignment by QIIME2, barplots, relative abundance tables, diversity analysis, differential abundance testing.

Skip taxonomic classification. Incompatible with --sbdiexport

Skip species level when using DADA2 for taxonomic classification. This reduces the required memory dramatically under certain conditions. Incompatible with --sbdiexport

Skip producing barplot

Skip producing any relative abundance tables

Skip alpha rarefaction

Skip alpha and beta diversity analysis

Skip differential abundance testing

Skip MultiQC reporting