github.com/nf-core/ampliseq

16S rRNA amplicon sequencing analysis workflow using QIIME2

=======================================================
                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~'
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

 nf-core/ampliseq : v
=======================================================

Usage:

The minimal command for running the pipeline is as follows:
nextflow run nf-core/ampliseq --reads "data" --FW_primer GTGYCAGCMGCCGCGGTAA --RV_primer GGACTACNVGGGTWTCTAAT --metadata "Metadata.tsv"


Required arguments:
  --reads [Path to folder]      Folder containing Casava 1.8 paired-end demultiplexed fastq files: *_L001_R{1,2}_001.fastq.gz
  --FW_primer [str]             Forward primer sequence
  --RV_primer [str]             Reverse primer sequence
  --metadata                    Path to metadata sheet

Filters:
  --exclude_taxa [str]          Comma seperated list of unwanted taxa (default: "mitochondria,chloroplast")
                                To skip filtering use "none"

Cutoffs:
  --retain_untrimmed            Cutadapt will retain untrimmed reads
  --trunclenf [int]             DADA2 read truncation value for forward strand
  --trunclenr [int]             DADA2 read truncation value for reverse strand
  --trunc_qmin [int]            If --trunclenf and --trunclenr are not set, 
                                these values will be automatically determined using 
                                this mean quality score (not preferred) (default: 25)

References:                     If you have trained a compatible classifier before
  --classifier                  Path to QIIME2 classifier file (typically *-classifier.qza)
  --classifier_removeHash       Remove all hash signs from taxonomy strings, resolves a rare ValueError during classification (process classifier)

Statistics:
  --metadata_category           Diversity indices will be calculated using these groupings in the metadata sheet,
                                all suitable columns in the metadata sheet will be used if not specified.
                                Suitable are columns which are categorical (not numerical) and have multiple  
                                different values which are not all unique.

Other options:
  --untilQ2import               Skip all steps after importing into QIIME2, used for visually choosing DADA2 parameter
  --Q2imported [Path]           Path to imported reads (e.g. "demux.qza"), used after visually choosing DADA2 parameter
  --onlyDenoising               Skip all steps after denoising, produce only sequences and abundance tables on ASV level

Skipping steps:
  --skip_fastqc                 Skip FastQC
  --skip_alpha_rarefaction      Skip alpha rarefaction
  --skip_taxonomy               Skip taxonomic classification
  --skip_barplot                Skip producing barplot
  --skip_abundance_tables       Skip producing any relative abundance tables
  --skip_diversity_indices      Skip alpha and beta diversity analysis
  --skip_ancom                  Skip differential abundance testing