Paquet : hisat2 (2.2.1-4 et autres)

[ Paquet source : hisat2  ]

graph-based alignment of short nucleotide reads to many genomes

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome). Based on an extension of BWT for graphs a graph FM index (GFM) was designed and implementd. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

Autres paquets associés à hisat2

• dep: libc6 (>= 2.34)

  bibliothèque C GNU : bibliothèques partagées
  un paquet virtuel est également fourni par libc6-udeb

• dep: libgcc-s1 (>= 4.2)

  bibliothèque de prise en charge de GCC

• dep: libstdc++6 (>= 11)

  bibliothèque standard C++ de GNU v3

• dep: perl

  langage de rapports et d'extractions pratiques de Larry Wall

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• rec: bcftools

  appel de variantes génomiques et manipulation de fichiers VCF et BCF

• rec: python3-hisat2

  Python scripts accompanying hisat2

• rec: samtools

  traitement d'alignements de séquence pour les formats SAM et BAM et CRAM

Télécharger hisat2

Télécharger pour toutes les architectures proposées

Architecture	Version	Taille du paquet	Espace occupé une fois installé	Fichiers
i386	2.2.1-4+b2	3 489,9 ko	14 726,0 ko	[liste des fichiers]