Snippy - T.Seemann - Poster - Genome Informatics 2016

Snippy - rapid haploid variant calling and core SNP alignments.

1. Snippy
Rapid bacterial variant calling
and core genome alignments
@torstenseemann
brew tap homebrew/science && brew install snippy
https://github.com/tseemann/snippy
TorstenSeemann, VLSCI, The University of Melbourne, AUSTRALIA
Command line
% snippy
--cpus32
--outdirout
--ref Ec_K12.gbk
--R1 ecoli_R1.fastq.gz
--R2 ecoli_R2.fastq.gz
% ls out
snps.vcfsnps.tabsnps.bam…
Etymology
It runs fast and SNAPPY
It finds variants like SNPs
Unique-ishin Google
Rhymes with SKIPPYthe bush kangaroo
Snippy core
Combine multiple Snippy runs into a
multiple sequence alignment in seconds
and build a phylogenomictree.
Pipelines –boring but useful!
Features
•Fast –4 min / 8 cores / 100x bacteria
•No need to trim Illumina adapters
•Bundled Linux and macOSbinaries
•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?