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Source: snippy
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
any2fasta <!nocheck>,
bcftools <!nocheck>,
bedtools <!nocheck>,
bwa <!nocheck>,
freebayes <!nocheck>,
libbio-perl-perl <!nocheck>,
libvcflib-tools <!nocheck>,
minimap2 <!nocheck>,
parallel <!nocheck>,
samtools <!nocheck>,
samclip <!nocheck>,
seqtk <!nocheck>,
snp-sites <!nocheck>,
snpeff <!nocheck>,
vt <!nocheck>
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/snippy
Vcs-Git: https://salsa.debian.org/med-team/snippy.git
Homepage: https://github.com/tseemann/snippy/
Rules-Requires-Root: no
Package: snippy
Architecture: all
Depends: ${perl:Depends},
${misc:Depends},
any2fasta,
bcftools,
bedtools,
bwa,
freebayes (>= 1.3.6-2),
libbio-perl-perl,
libvcflib-tools,
minimap2,
parallel,
samclip,
samtools,
seqtk,
snp-sites,
snpeff,
vt
Description: 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).
Package: snippy-examples
Architecture: all
Depends: ${misc:Depends}
Recommends: snippy
Multi-Arch: foreign
Description: rapid haploid variant calling and core genome alignment (examples)
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).
.
This package contains example data to test snippy.
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