Paket: hisat2 (2.2.1-5) [debports]

[ Quellcode:  ]

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).

Andere Pakete mit Bezug zu hisat2

• dep: libc6 (>= 2.38)

  GNU-C-Bibliothek: Laufzeitbibliotheken
  auch ein virtuelles Paket, bereitgestellt durch libc6-udeb

• dep: libgcc-s1 (>= 3.0)

  GCC Support-Bibliothek

• dep: libstdc++6 (>= 13.1)

  GNU-Implementierung der Standard-C++-Bibliothek (Version 3)

• dep: perl

  Larry Wall's Practical Extraction und Report Language

• dep: python3

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

• rec: bcftools

  Aufruf und Manipulation genomischer Varianten von VCF/BCF-Dateien

• rec: python3-hisat2

  Python scripts accompanying hisat2

• rec: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

hisat2 herunterladen

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Architektur	Paketgröße	Größe (installiert)	Dateien
ppc64 (inoffizielle Portierung)	3.507,0 kB	14.186,0 kB	[Liste der Dateien]