1.4.2

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

Additional tools (optional):

• minimap2 2.24+dfsg-2
• bwa 0.7.17-6

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

Starting with iVar version 1.4.1, the output of an aligner such as minimap2 and bwa (both included) can be piped into ivar trim directly

# index reference
bwa index reference.fasta

# run bwa and pipe into ivar (single line is split with \ for clarity)
bwa mem reference.fasta read_1.fastq.gz read_2.fastq.gz | \
  ivar trim -b primer.bed -x 3 -m 30 | \
  samtools sort | \
  samtools mpileup -aa -A -Q 0 -B -d 2000 - | \
  ivar consensus -p output_prefix -m 10 -n N -t 0.5