<![CDATA[BOL: Snippy: Rapid haploid variant calling and core SNP phylogeny]]> https://bioinformaticsonline.com/bookmarks/view/37536/snippy-rapid-haploid-variant-calling-and-core-snp-phylogeny? https://bioinformaticsonline.com/bookmarks/view/37536/snippy-rapid-haploid-variant-calling-and-core-snp-phylogeny Sat, 11 Aug 2018 11:06:56 -0500 https://bioinformaticsonline.com/bookmarks/view/37536/snippy-rapid-haploid-variant-calling-and-core-snp-phylogeny <![CDATA[Snippy: Rapid haploid variant calling and core SNP phylogeny]]> Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is designed with speed in mind, and produces a consistent set of output files in a single folder. It can then take a set of Snippy results using the same reference and generate a core SNP alignment (and ultimately a phylogenomic tree).

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

Address of the bookmark: https://github.com/tseemann/snippy

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