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