Ragout
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.
Environment Modules
Run module spider ragout to find out what environment modules are available for this application.
System Variables
- HPC_RAGOUT_DIR - installation directory