Пакет: snippy (4.6.0+dfsg-4)

Ссылки для snippy

Ресурсы Debian:

Исходный код snippy:

Сопровождающие:

Внешние ресурсы:

Сайт [github.com]

Подобные пакеты:

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).

Другие пакеты, относящиеся к snippy

зависимости

рекомендации

предложения

enhances

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

параллельное выполнение команд
dep: perl

практический язык Ларри Уолла для извлечения данных и составления отчётов
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

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