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nf-core/shotgunmetagenomics: Output

This document describes the output produced by the pipeline.

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps:

Fastp

Fastp performs adapter removal and low quality base trimming. This step is streamed to the next decontamination step.

Output directory: pipeline_output/decont/

  • sample.html and sample.json
    • Fastp report

Decontamination

This step takes the Fastp output, maps the reads to the host reference genome provided and outputs only the unmapped reads.

Output directory: pipeline_output/decont/

  • sample_fastpdecont_1.fastq.gz and sample_fastpdecont_2.fastq.gz
    • Unmapped reads by the pipeline

Kraken2

Kraken2 assign taxonomy to reads (read pairs) based on K-mer profile.

Output directory: pipeline_output/kraken2_out

  • sample.kraken2.report
    • Plain text file for standard Kraken2 report
  • sample.kraken2.tax
    • Plain text file for MetaPhlAn-like taxonomic profile (in read counts)

Split table into taxonomic levels: pipeline_output/split_kraken2_out

  • sample.[dpcofgs].tsv
  • Plain text files for taxonomic profile at domain, phylum, class, order, family, genus, species, respectively

Bracken

Bracken estimates relative abundances of taxa based on a Kraken2 report.

Output directory: pipeline_output/bracken_out

  • sample.bracken.g.tsv
    • Tab-delimited text file for genus level relative abundances
  • sample.bracken.s.tsv
    • Tab-delimited text file for species level relative abundances

StrainPhlAn

StrainPhlAn is a strain analysis workflow based on SNP.

Output directory: pipeline_output/strainphlan_out

  • sample.metaphlan2.markers
    • Marker files for each sample

MetaPhlAn2

MetaPhlAn2 estimates relative abundances of taxa by mapping reads to clade-specific marker genes.

Output directory: pipeline_output/metaphlan2_out

  • sample.metaphlan2.tax
    • Tab-delimited text file for the full taxonomic profile

Split table into taxonomic levels: pipeline_output/split_metaphlan2_out

  • sample.[dpcofgs].tsv
  • Plain text files for taxonomic profile at domain, phylum, class, order, family, genus, species, respectively

HUMAnN2

HUMAnN2 estimates gene family and pathway abundances.

Output directory: pipeline_output/humann2_out

  • sample.humann2_genefamilies.tsv and sample.humann2_genefamilies.relab.tsv
    • Tab-delimited text file for the raw and normalized gene family abundances
  • sample.humann2_pathabundance.tsv and sample.humann2_pathabundance.relab.tsv
    • Tab-delimited text file for the raw and normalized pathway abundances
  • sample.humann2_pathcoverage.tsv
    • Tab-delimited text file for the pathway coverage

SRST2

SRST2 reports the presence of antibiotics resistance genes.

Output directory: pipeline_output/srst2_out

  • sample__fullgenes__ARGannot.r3__results.txt
    • Tab-delimited text file for the full report
  • sample__genes__ARGannot.r3__results.txt
    • Tab-delimited text file for the simplified report
  • sample__ARGannot.r3__results.sorted.bam
    • BAM file for alignments

See here for details