MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

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 metagenome assembly, which we called 'MetaVelvet', for mixed short reads of multiple species. Our fundamental concept was to first decompose a de Bruijn graph…

• MO
  Ministry of Education, Culture, Sports, Science and Technology

  Award: 221S0002
• JS
  Japan Society for the Promotion of Science

  Award: 221S0002
• JS
  Japan Science and Technology Agency