Pakket: hisat2 (2.2.1-5~0exp)
Verwijzigingen voor hisat2
Debian bronnen:
Het bronpakket hisat2 downloaden:
Beheerders:
Externe bronnen:
- Homepage [daehwankimlab.github.io]
Vergelijkbare pakketten:
Experimenteel pakket
Warning: This package is from the experimental distribution. That means it is likely unstable or buggy, and it may even cause data loss. Please be sure to consult the changelog and other possible documentation before using it.
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 aan hisat2 gerelateerde pakketten
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- dep: libc6 (>= 2.34)
- GNU C Bibliotheek: Gedeelde bibliotheken
Ook een virtueel pakket geboden door: libc6-udeb
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- dep: libgcc-s1 (>= 3.5)
- GCC support bibliotheek
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- dep: libstdc++6 (>= 11)
- GNU Standard C++ Library v3
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- dep: perl
- Larry Wall's Practical Extraction and Report Language
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- dep: python3
- interactive high-level object-oriented language (default python3 version)
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- rec: bcftools
- genomic variant calling and manipulation of VCF/BCF files
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- rec: python3-hisat2
- Python scripts accompanying hisat2
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- rec: samtools
- processing sequence alignments in SAM, BAM and CRAM formats