Generate a consensus sequence from a BAM file using iVar
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam:file
A sorted (with samtools sort) and trimmed (with iVar trim) bam file
*.bam
fasta:file
The reference sequence used for mapping and generating the BAM file
*.fa
save_mpileup:boolean
Save mpileup file generated by ivar consensus
fasta
*.fa:file
iVar generated consensus sequence
qual
*.qual.txt:file
iVar generated quality file
*.qual.txt
mpileup
*.mpileup:file
mpileup output from samtools mpileup [OPTIONAL]
*.mpileup
versions
versions.yml:file
File containing software versions
versions.yml
iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.
