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Paquet : hisat2 (2.2.1-3)

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

  • dépendances
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  • dep: libc6 (>= 2.34)
    GNU C Library: Shared libraries
    un paquet virtuel est également fourni par libc6-udeb
  • dep: libgcc-s1 (>= 3.3.1) [non armhf]
    GCC support library
    dep: libgcc-s1 (>= 3.5) [armhf]
  • dep: libstdc++6 (>= 11)
    GNU Standard C++ Library v3
  • dep: perl
    Larry Wall's Practical Extraction and Report Language
  • dep: python3
    interactive high-level object-oriented language (default python3 version)
  • rec: bcftools
    genomic variant calling and manipulation of VCF/BCF files
  • rec: python3-hisat2
    Python scripts accompanying hisat2
  • rec: samtools
    processing sequence alignments in SAM, BAM and CRAM formats

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amd64 3 742,3 ko12081 ko [liste des fichiers]
arm64 3 940,2 ko11305 ko [liste des fichiers]
armhf 3 996,4 ko11485 ko [liste des fichiers]
ppc64el 4 149,5 ko12233 ko [liste des fichiers]