idba
iterative De Bruijn Graph short read assemblers
Command lineScience
Not tested on a device yet. What that means
Commands in the package
idbaidba_hybrididba_tranidba_ud
About idba
From Debian's package description
IDBA stands for iterative de Bruijn graph assembler. In computational sequence biology, an assembler solves the puzzle coming from large sequencing machines that feature many gigabytes of short reads from a large genome.
This package provides several flavours of the IDBA assembler, as they all share the same source tree but serve different purposes and evolved over time.
IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a generic purpose assembler and especially good for single-cell and metagenomic sequencing data. IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for RNA-Seq data.
From Debian's description of the idba package, under that package's license.
Dependencies
Depends on
libc6libgcc-s1libgomp1libstdc++6python3
Related apps
- idba-extraiterative De Bruijn Graph short read assemblers (extra tools)Command line
- bowtie2ultrafast memory-efficient short read alignerCommand line
- bowtieUltrafast memory-efficient short read alignerCommand line
- hisat2graph-based alignment of short nucleotide reads to many genomesCommand line
- macsModel-based Analysis of ChIP-Seq on short reads sequencersCommand line
- roaryhigh speed stand alone pan genome pipelineCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the idba package, under that package's license.
- Description: Debian's description of the idba package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.