[ sid ]
[ 源代码： snippy ]
软件包：snippy（4.6.0+dfsg-5）
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).
其他与 snippy 有关的软件包
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- dep: any2fasta
- convert various sequence formats to FASTA
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- dep: bcftools
- genomic variant calling and manipulation of VCF/BCF files
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- dep: bedtools
- suite of utilities for comparing genomic features
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- dep: bwa
- Burrows-Wheeler Aligner
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- dep: freebayes (>= 1.3.6-2)
- Bayesian haplotype-based polymorphism discovery and genotyping
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- dep: libbio-perl-perl
- BioPerl core perl modules
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- dep: libvcflib-tools
- C++ library for parsing and manipulating VCF files (tools)
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- dep: minimap2
- versatile pairwise aligner for genomic and spliced nucleotide sequences
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- dep: parallel
- build and execute command lines from standard input in parallel
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- dep: perl
- 拉里 沃尔的实用报表提取语言(Perl)
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- dep: samclip
- filter SAM file for soft and hard clipped alignments
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- dep: samtools
- processing sequence alignments in SAM, BAM and CRAM formats
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- dep: seqtk
- Fast and lightweight tool for processing sequences in the FASTA or FASTQ format
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- dep: snp-sites
- Binary code for the package snp-sites
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- dep: snpeff
- genetic variant annotation and effect prediction toolbox - tool
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- dep: vt
- toolset for short variant discovery in genetic sequence data