Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

Recent advances in single-cell genomics provide an alternative to largely gene-centric metagenomics studies, enabling whole-genome sequencing of uncultivated bacteria. However, single-cell assembly projects are challenging due to (i) the highly nonuniform read coverage and (ii) a greatly elevated number of chimeric reads and read pairs. While recently developed single-cell assemblers have addressed the former challenge, methods for assembling highly chimeric reads remain poorly explored. We present algorithms for identifying chimeric edges and resolving complex bulges in de Bruijn graphs, which significantly improve single-cell assemblies. We further describe applications of the single-cell assembler SPAdes to…

• NS
  National Science Foundation

  Awards: 1148017, DE-AC02-05CH11231, 1115206
• UD
  U.S. Department of Energy

  Awards: -AC02-05CH11231, 05CH11231, AC02-05CH11231, DE-AC02, DE-AC02-05CH11231, DE-AC02-
• AP
  Alfred P. Sloan Foundation

  Award: DE-AC02-05CH11231
• NI
  National Institutes of Health

  Award: DE-AC02-05CH11231
• OO
  Office of Science

  Awards: AC02-05CH11231, -AC02-05CH11231, DE-AC02