snippy - t.seemann - poster - genome informatics 2016
Post on 19-Feb-2017
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SnippyRapid bacterial variant calling and core genome alignments
@torstenseemann
brew tap homebrew/science && brew install snippy
https://github.com/tseemann/snippy
Torsten Seemann, VLSCI, The University of Melbourne, AUSTRALIA
Command line
% snippy--cpus 32--outdir out--ref Ec_K12.gbk--R1 ecoli_R1.fastq.gz--R2 ecoli_R2.fastq.gz
% ls outsnps.vcf snps.tab snps.bam …
Etymology
It runs fast and SNAPPY
It finds variants like SNPs
Unique-ish in Google
Rhymes with SKIPPY the bush kangaroo
Snippy core
Combine multiple Snippy runs into amultiple sequence alignment in seconds
and build a phylogenomic tree.
Pipelines – boring but useful!
Features
• Fast – 4 min / 8 cores / 100x bacteria
• No need to trim Illumina adapters
• Bundled Linux and macOS binaries
• Standard input and output
• Detailed variant report
• Documentation (yes!)
VCFBAMTXT
FASTQFASTA
GBK
BWA MEMSAMtoolsFreeBayes
VCFlibsnpEff
Competitors
PHEnixPilon
BreseqVarscanBCFtools
Slower,but better?
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