Call细菌SNP用Snippy

从reads/contig中call细菌突变

Github: https://github.com/tseemann/snippy

安装

conda create -n snippy
conda activate snippy
snippy -h
# snippy 4.6.0 - fast bacterial variant calling from NGS reads

USAGE
  snippy [options] --outdir <dir> --ref <ref> --R1 <R1.fq.gz> --R2 <R2.fq.gz>
  snippy [options] --outdir <dir> --ref <ref> --ctgs <contigs.fa>
  snippy [options] --outdir <dir> --ref <ref> --bam <reads.bam>

懒得测试了，直接抄代码

从一个样本/基因组中call snp

snippy \
--cpus 16 \
--outdir mysnps \
--ref Listeria.gbk \
--R1 FDA_R1.fastq.gz 
--R2 FDA_R2.fastq.gz

从多个样本/基因组中call core snp

输入文件格式：支持单端，双端，组装文件

# input.tab = ID R1 [R2]
Isolate1    /path/to/R1.fq.gz   /path/to/R2.fq.gz
Isolate1b   /path/to/R1.fastq.gz    /path/to/R2.fastq.gz
Isolate1c   /path/to/R1.fa      /path/to/R2.fa
# single end reads supported too
Isolate2    /path/to/SE.fq.gz
Isolate2b   /path/to/iontorrent.fastq
# or already assembled contigs if you don't have reads
Isolate3    /path/to/contigs.fa
Isolate3b   /path/to/reference.fna.gz

使用

snippy-multi input.tab \
--ref Reference.gbk \
--cpus 16 \
> runme.sh
less runme.sh   # check the script makes sense
sh ./runme.sh   # leave it running over lunch 有趣的灵魂

突变类型

高级使用
Increasing speed when too many reads
Only calling SNPs in particular regions
Finding SNPs between contigs

参考
使用Snippy构建细菌基因组SNP、core SNP和系统进化分析