Package: hisat2 (2.2.1-2 and others)
Links for hisat2
Debian Resources:
Download Source Package hisat2:
Maintainers:
External Resources:
- Homepage [daehwankimlab.github.io]
Similar packages:
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).
Other Packages Related to hisat2
|
|
|
|
-
- dep: libc6 (>= 2.29)
- GNU C Library: Shared libraries
also a virtual package provided by libc6-udeb
-
- dep: libgcc-s1 (>= 3.5)
- GCC support library
-
- dep: libstdc 6 (>= 9)
- 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
Download hisat2
| Architecture | Version | Package Size | Installed Size | Files |
|---|---|---|---|---|
| armel | 2.2.1-2 b3 | 3,282.8 kB | 12,932.0 kB | [list of files] |