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

]

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

meta (map)

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

]

bam (file)

iVar generated trimmed bam file (unsorted)

*.bam

log (file)

Log file generated by iVar for use with MultiQC

*.log

versions (file)

File containing software versions

versions.yml
included in
viralrecon
authors
Github user andersgs Github user drpatelh
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

ivar
GPL-3.0-or-later

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

github.com/andersen-lab/ivar andersen-lab.github.io/ivar/html/manualpage