minidna

Présentation

minidna (mini-contig de novo assembly) is a command line tool to quickly inƒer small circular contigs (e.g. < 10,000 bps) ƒrom long-read whole genome sequencing data.

In a nutshell, minidna ƒirst searches for subset(s) of circular reads deriving ƒrom the same contig, and next inƒers the circular contig corresponding to each long-read subset. As this simple approach runs ƒast and requires few dependencies, minidna can then be used in addition to any long-read-only and/or long-read-ƒirst assemblers in order to compensate their potential ƒailure to recover small plasmids.

minidna is ƒreely available at gitlab.pasteur.fr/GIPhy/minidna. It runs on Linux and most OS X operating systems.