ragout
Reference-Assisted Genome Ordering UTility
Command lineScience
Not tested on a device yet. What that means
Commands in the package
ragoutragout-maf2syntenyragout-overlap
About ragout
From Debian's package description
Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome-level scaffolding using multiple references. Given initial assembly fragments (contigs/scaffolds) and one or multiple related references (complete or draft), it produces a chromosome-scale assembly (as a set of scaffolds).
The approach is based on the analysis of genome rearrangements (like inversions or chromosomal translocations) between the input genomes and reconstructing the most parsimonious structure of the target genome.
Ragout now supports both small and large genomes (of mammalian scale and complexity). The assembly of highly polymorphic genomes is currently limited.
From Debian's description of the ragout package, under that package's license.
Dependencies
Depends on
libc6libgcc-s1libstdc++6python3python3-networkxpython3-six
Recommends
Related apps
- metisSerial Graph Partitioning and Fill-reducing Matrix Ordering. BinariesCommand line
- plasmididmapping-based, assembly-assisted plasmid identification toolCommand line
- damapperlong read to reference genome mapping toolCommand line
- seqprepstripping adaptors and/or merging paired reads of DNA sequences with overlapCommand line
- artfastqgeneratoroutputs artificial FASTQ files derived from a reference genomeCommand line
- rsemRNA-Seq by Expectation-MaximizationCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the ragout package, under that package's license.
- Description: Debian's description of the ragout 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.