1.2.2_artic20200528

iVar container

Main tool : iVar

Additional tools:

• seqtk
• Minimap2
• HTSlib
• samtools
• bwa
• snakemake

Also includes the

• artic primers as they were on 2020-05-28 (ef3f1ce9f66d49ec7caa67e0425e556bd67c53de)
• A bedfile representing the amplicons (alt primers are ignored) at /artic-ncov2019/primer_schemes/nCoV-2019/{V1,V2,V3}/nCoV-2019_amplicon.bed
• A gff file for the reference sequence /reference/GCF_009858895.2_ASM985889v3_genomic.gff.gz

Example Usage

ivar trim -e -i {bam} -b /artic-ncov2019/primer_schemes/nCoV-2019/V3/nCoV-2019.bed -p {sample}.primertrim

samtools mpileup -A -d 600000 -B -Q 0 --reference /artic-ncov2019/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta {bam} | \
      ivar variants -p {sample}.variants -q 20 -t 0.6 -r /artic-ncov2019/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta -g /reference/GCF_009858895.2_ASM985889v3_genomic.gff

samtools mpileup -A -d 6000000 -B -Q 0 --reference /artic-ncov2019/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta {bam} | \
      ivar consensus -t 0.6 -p {sample}.consensus -n N