Description

Trim primer sequences rom a BAM file with iVar

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

bam:file

Co-ordinate sorted BAM file

*.bam

bai:file

Index file for co-ordinate sorted BAM file

*.bai

bed:file

BED file with primer labels and positions

*.bed

Output

name:type
description
pattern

bam

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.bam:file

iVar generated trimmed bam file (unsorted)

*.bam

log

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.log:file

Log file generated by iVar for use with MultiQC

*.log

versions

versions.yml:file

File containing software versions

versions.yml

Tools

ivar
GPL-3.0-or-later

iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.