ragout - 2.3-5+b2 main

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).
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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.
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Ragout now supports both small and large genomes (of mammalian scale
and complexity). The assembly of highly polymorphic genomes is
currently limited.