Package: snippy (4.6.0+dfsg-4)

[ Source: snippy  ]

rapid haploid variant calling and core genome alignment

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).

Other Packages Related to snippy

• dep: any2fasta

  convert various sequence formats to FASTA

• dep: bcftools

  genomic variant calling and manipulation of VCF/BCF files

• dep: bedtools

  suite of utilities for comparing genomic features

• dep: bwa

  Burrows-Wheeler Aligner

• dep: freebayes (>= 1.3.6-2)

  Bayesian haplotype-based polymorphism discovery and genotyping

• dep: libbio-perl-perl

  BioPerl core perl modules

• dep: libvcflib-tools

  C++ library for parsing and manipulating VCF files (tools)

• dep: minimap2

  versatile pairwise aligner for genomic and spliced nucleotide sequences

• dep: parallel

  build and execute command lines from standard input in parallel

• dep: perl

  Larry Wall's Practical Extraction and Report Language

• dep: samclip

  filter SAM file for soft and hard clipped alignments

• dep: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• dep: seqtk

  Fast and lightweight tool for processing sequences in the FASTA or FASTQ format

• dep: snp-sites

  Binary code for the package snp-sites

• dep: snpeff

  genetic variant annotation and effect prediction toolbox - tool

• dep: vt

  toolset for short variant discovery in genetic sequence data

Download snippy

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Architecture	Package Size	Installed Size	Files
all	26.2 kB	100.0 kB	[list of files]