An extension of Velvet assembler to de novo metagenomic assembly. An important step in metagenomics analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines use a single-genome assembler with carefully optimized parameters. A limitation of a single-genome assembler for de novo metagenome assembly is that sequences of highly abundant species are likely misidentified as repeats in a single genome, resulting in a number of small fragmented scaffolds. We extended a single-genome assembler for short reads, known as Velvet, to metagenomic assembly for mixed short reads of multiple species.
module add metaVelvet-1.2
This makes available the path to the program binaries.
GNU GPL 3