Snippy - T.Seemann - Poster - Genome Informatics 2016
1
Snippy Rapid 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 out snps.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 a multiple 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!) VCF BAM TXT FASTQ FASTA GBK BWA MEM SAMtools FreeBayes VCFlib snpEff Competitors PHEnix Pilon Breseq Varscan BCFtools Slower, but better?
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Transcript of Snippy - T.Seemann - Poster - Genome Informatics 2016
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?
