fermi-lite

Library and tool for assembling Illumina short reads in small regions

Fermi-lite is a standalone C library as well as a command-line tool for assembling Illumina short reads in regions from 100bp to 10 million bp in size. It is largely a light-weight in-memory version of fermikit without generating any intermediate files. It inherits the performance, the relatively small memory footprint and the features of fermikit. In particular, fermi-lite is able to retain heterozygous events and thus can be used to assemble diploid regions for the purpose of variant calling. It is one of the limited choices for local re-assembly and arguably the easiest to interface.