README.md

iVar container

Main tool : iVar

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

Additional tools (required):

• HTSlib 1.17
• samtools 1.17
• bedtools 2.30.0
• python 3.10.6

Example Usage

ivar trim -e -i {bam} -b {primer bed} -p {sample}.primertrim

samtools mpileup -A -d 8000 -B -Q 0 --reference {reference.fasta} {bam} | \
      ivar variants -p {sample}.variants -q 20 -t 0.6 -r {reference.fasta} -g {reference.gff}

samtools mpileup -A -d 8000 -B -Q 0 --reference {reference.fasta} {bam} | \
      ivar consensus -t 0.6 -p {sample}.consensus -n N