GraphBin2: Refined and overlapped binning of metagenomic contigs using assembly graphs

Vijini G. Mallawaarachchi, Anuradha S. Wickramarachchi, Yu Lin

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

5 Citations (Scopus)
3 Downloads (Pure)

Abstract

Metagenomic sequencing allows us to study structure, diversity and ecology in microbial communities without the necessity of obtaining pure cultures. In many metagenomics studies, the reads obtained from metagenomics sequencing are first assembled into longer contigs and these contigs are then binned into clusters of contigs where contigs in a cluster are expected to come from the same species. As different species may share common sequences in their genomes, one assembled contig may belong to multiple species. However, existing tools for contig binning only support non-overlapped binning, i.e., each contig is assigned to at most one bin (species). In this paper, we introduce GraphBin2 which refines the binning results obtained from existing tools and, more importantly, is able to assign contigs to multiple bins. GraphBin2 uses the connectivity and coverage information from assembly graphs to adjust existing binning results on contigs and to infer contigs shared by multiple species. Experimental results on both simulated and real datasets demonstrate that GraphBin2 not only improves binning results of existing tools but also supports to assign contigs to multiple bins.

Original languageEnglish
Title of host publication20th International Workshop on Algorithms in Bioinformatics, WABI 2020
EditorsCarl Kingsford, Nadia Pisanti
PublisherSchloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
Number of pages21
ISBN (Electronic)9783959771610
DOIs
Publication statusPublished - 25 Aug 2020
Externally publishedYes
Event20th International Workshop on Algorithms in Bioinformatics, WABI 2020 - Virtual, Pisa, Italy
Duration: 7 Sep 20209 Sep 2020

Publication series

NameLeibniz International Proceedings in Informatics, LIPIcs
Volume172
ISSN (Print)1868-8969

Conference

Conference20th International Workshop on Algorithms in Bioinformatics, WABI 2020
Country/TerritoryItaly
CityVirtual, Pisa
Period7/09/209/09/20

Keywords

  • Assembly graphs
  • Contigs
  • Metagenomics binning
  • Overlapped binning
  • GraphBin2

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