output.md

nf-core/vipr

This document describes the output produced by the pipeline. Results will appear in the directory specified with the --outdir parameter (default: results). Each sample has its own subdirectory. The structure of a sample subdirectory is described in the following.

Read Data

Reads are preprocessed, i.e. quality trimmed (and combined in case of multiple read pairs) as well as decontaminated. All respective data is stored in the reads/ sub-directory

• reads/{sample}_R[12]-trimmed.fastq.gz: quality trimmed (and combined) reads
• reads/{sample}_trimmed_decont_[12].fastq.gz: decontaminated trimmed reads
• reads/{sample}_trimmed_decont_[12]_fastqc.*: fastqc data for the above

Assembly

Preprocessed reads are assembled into contig and then orientated and glued together using the user-specified reference. As a final step the assembly is polished through iterative mapping, consensus calling and variant integration

• {sample}_contigs.fa: Tadpole contigs
• {sample}-gap-filled-assembly.fa: Orientated contigs, gaps filled with reference
• {sample}-gap-filled-assembly.gaps.bed: reference gap positions
• {sample}_polished_assembly.fa: Assembly polished through iterative mapping, consensus calling and variant integration
• {sample}_0cov2N.fa: submission-ready reference with zero coverage positions masked

Mapping and variant calling

• {sample}_kraken.report.txt: Kraken report
• {sample}.cov.gz: Coverage per position
• {sample}.bam: Preprocessed reads mapped against polished assembly
• {sample}.bam.bai: BAM index
• {sample}.bam.stats: Stats for BAM file
• {sample}.vcf.gz: LoFreq variant calls for BAM file
• {sample}_af-vs-cov.html: Interactive plot of variant AF vs coverage

A screenshot of the interative plot follows: