Improving metagenomic binning results with overlapped bins using assembly graphs
Abstract Background Metagenomic sequencing allows us to study the 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 thes...
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| Format: | Article |
| Language: | English |
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BMC
2021-05-01
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| Series: | Algorithms for Molecular Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13015-021-00185-6 |
| _version_ | 1819298447888482304 |
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| author | Vijini G. Mallawaarachchi Anuradha S. Wickramarachchi Yu Lin |
| author_facet | Vijini G. Mallawaarachchi Anuradha S. Wickramarachchi Yu Lin |
| author_sort | Vijini G. Mallawaarachchi |
| collection | DOAJ |
| description | Abstract Background Metagenomic sequencing allows us to study the 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 binning contigs only support non-overlapped binning, i.e., each contig is assigned to at most one bin (species). Results 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. Conclusion GraphBin2 incorporates the coverage information into the assembly graph to refine the binning results obtained from existing binning tools. GraphBin2 also enables the detection of contigs that may belong to multiple species. We show that GraphBin2 outperforms its predecessor GraphBin on both simulated and real datasets. GraphBin2 is freely available at https://github.com/Vini2/GraphBin2 . |
| first_indexed | 2024-12-24T05:30:03Z |
| format | Article |
| id | doaj.art-d98a6b9809b74644bb75eab451166ff9 |
| institution | Directory Open Access Journal |
| issn | 1748-7188 |
| language | English |
| last_indexed | 2024-12-24T05:30:03Z |
| publishDate | 2021-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Algorithms for Molecular Biology |
| spelling | doaj.art-d98a6b9809b74644bb75eab451166ff92022-12-21T17:13:12ZengBMCAlgorithms for Molecular Biology1748-71882021-05-0116111810.1186/s13015-021-00185-6Improving metagenomic binning results with overlapped bins using assembly graphsVijini G. Mallawaarachchi0Anuradha S. Wickramarachchi1Yu Lin2School of Computing, College of Engineering and Computer Science, Australian National UniversitySchool of Computing, College of Engineering and Computer Science, Australian National UniversitySchool of Computing, College of Engineering and Computer Science, Australian National UniversityAbstract Background Metagenomic sequencing allows us to study the 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 binning contigs only support non-overlapped binning, i.e., each contig is assigned to at most one bin (species). Results 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. Conclusion GraphBin2 incorporates the coverage information into the assembly graph to refine the binning results obtained from existing binning tools. GraphBin2 also enables the detection of contigs that may belong to multiple species. We show that GraphBin2 outperforms its predecessor GraphBin on both simulated and real datasets. GraphBin2 is freely available at https://github.com/Vini2/GraphBin2 .https://doi.org/10.1186/s13015-021-00185-6Metagenomics binningContigsAssembly graphsOverlapped binning |
| spellingShingle | Vijini G. Mallawaarachchi Anuradha S. Wickramarachchi Yu Lin Improving metagenomic binning results with overlapped bins using assembly graphs Algorithms for Molecular Biology Metagenomics binning Contigs Assembly graphs Overlapped binning |
| title | Improving metagenomic binning results with overlapped bins using assembly graphs |
| title_full | Improving metagenomic binning results with overlapped bins using assembly graphs |
| title_fullStr | Improving metagenomic binning results with overlapped bins using assembly graphs |
| title_full_unstemmed | Improving metagenomic binning results with overlapped bins using assembly graphs |
| title_short | Improving metagenomic binning results with overlapped bins using assembly graphs |
| title_sort | improving metagenomic binning results with overlapped bins using assembly graphs |
| topic | Metagenomics binning Contigs Assembly graphs Overlapped binning |
| url | https://doi.org/10.1186/s13015-021-00185-6 |
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