[ sid ]
[ ソース: snippy ]
パッケージ: snippy (4.6.0+dfsg-4)
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).
その他の snippy 関連パッケージ
|
|
|
|
-
- dep: any2fasta
- convert various sequence formats to FASTA
-
- dep: bcftools
- ゲノムの variant call と VCF/BCF ファイルの操作
-
- 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 作の実用的な抽出とレポート用の言語
-
- 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