nf-core/ampliseq

Path to tab-separated sample sheet

Path to ASV/OTU fasta file

Path to 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, …).

Path to multi-region definition sheet, for multi-region analysis with Sidle

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

Save intermediate results such as QIIME2’s qza and qzv files

Email address for completion summary.

If data has binned quality scores such as Illumina NovaSeq

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

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

Type of quality scores in raw read data

If using --input_folder: samples were sequenced in multiple sequencing runs

If using --input_folder: naming of sequencing files

Set read count threshold for failed samples.

Ignore input files with too few reads.

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

Sets the minimum overlap for valid matches of primer sequences with reads for cutadapt (-O).

Sets the maximum error rate for valid matches of primer sequences with reads for cutadapt (-e).

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

Ignore files with too few reads after trimming.

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

Ignore files with too few reads after quality filtering.

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

Strategy to merge paired end reads. When paired end reads are not sufficiently overlapping for merging, you can use “concatenate” (not recommended). When you have a mix of overlapping and non overlapping reads use “consensus”

The score assigned for each matching base pair during sequence alignment.

The penalty score assigned for each mismatched base pair during sequence alignment.

The penalty score assigned for each gap introduced during sequence alignment.

The minimum number of overlapping base pairs required to merge forward and reverse reads.

The maximum number of mismatches allowed within the overlapping region for merging reads.

The percentile used to determine a stringent cutoff which will correspond to the minimum observed overlap in the dataset. This ensures that only read pairs with high overlap are merged into consensus sequences. Those with insufficient overlap are concatenated.

Post-cluster ASVs with VSEARCH

Pairwise Identity value used when post-clustering ASVs if --vsearch_cluster option is used (default: 0.97).

Raise stack size when filtering VSEARCH clusters

Enable SSU filtering. Comma separated list of kingdoms (domains) in Barrnap, a combination (or one) of “bac”, “arc”, “mito”, and “euk”. ASVs that have their lowest evalue in that kingdoms are kept.

Minimal ASV length

Maximum ASV length

Filter ASVs based on codon usage

Starting position of codon tripletts

Ending position of codon tripletts

Define stop codons

Name of supported database, and optionally also version number

Path to a custom DADA2 reference taxonomy database

Path to a custom DADA2 reference taxonomy database for species assignment

Comma separated list of taxonomic levels used in DADA2’s assignTaxonomy function

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

If multiple exact matches against different species are returned

If reverse-complement of each sequences will be also tested for classification

ASV fasta will be subset into chunks of this size for classification

Newick file with reference phylogenetic tree. Requires also --pplace_aln and --pplace_model.

File with reference sequences. Requires also --pplace_tree and --pplace_model.

Phylogenetic model to use in placement, e.g. ‘LG+F’ or ‘GTR+I+F’. Requires also --pplace_tree and --pplace_aln.

Method used for alignment, “hmmer” or “mafft”

Tab-separated file with taxonomy assignments of reference sequences.

Name of supported database, and optionally also version number

Path to files of a custom QIIME2 reference taxonomy database (tarball, or two comma-separated files)

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

Name of supported database, and optionally also version number

Path to a custom Kraken2 reference taxonomy database (.tar.gz|.tgz archive or folder)

Comma separated list of taxonomic levels used in Kraken2. Will overwrite default values.

Confidence score threshold for taxonomic classification.

Name of supported database, and optionally also version number

If ASVs should be assigned to UNITE species hypotheses (SHs). Only relevant for ITS data.

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

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

Name of supported database, and optionally also version number

Path to reference taxonomy strings (headerless, *.txt)

Path to reference taxonomy sequences in fasta format

Path to multiple sequence alignment of reference taxonomy sequences in fasta format

Path to SIDLE reference taxonomy tree (*.qza)

Exclude reference sequences with more than this much degenerates

Arguments for qiime sidle reconstruct-taxonomy regarding ad-hoc cleaning

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.

Comma separated list of metadata column headers for plotting average relative abundance barplots.

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

If the functional potential of the bacterial community is predicted.

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

Minimum rarefaction depth for diversity analysis. Any sample below that threshold will be removed.

Minimum taxonomy agglomeration level for taxonomic classifications

Maximum taxonomy agglomeration level for taxonomic classifications

Minimum sample counts to retain a sample for ANCOM analysis. Any sample below that threshold will be removed.

Perform differential abundance analysis with ANCOM

Perform differential abundance analysis with ANCOMBC

Formula to perform differential abundance analysis with ANCOMBC

Reference level for --ancombc_formula

Effect size threshold for differential abundance barplot for --ancombc and --ancombc_formula

Significance threshold for differential abundance barplot for --ancombc and --ancombc_formula

Path to Markdown file (Rmd)

Path to style file (css)

Path to logo file (png)

String used as report title

Path to Markdown file (md) that replaces the ‘Abstract’ section

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 quality check with DADA2. Can only be skipped when --trunclenf and --trunclenr are set.

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 steps that are executed by QIIME2 except for taxonomic classification. Skip steps including barplots, relative abundance tables, diversity analysis, differential abundance testing.

Skip taxonomic classification. Incompatible with --sbdiexport

Skip taxonomic classification with DADA2

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 exporting phyloseq rds object(s)

Skip exporting TreeSummarizedExperiment rds object(s)

Skip MultiQC reporting

Skip Markdown summary report

Specifies the random seed.

Custom MultiQC yaml file containing HTML including a methods description.