HairSplitter: haplotype assembly from long, noisy reads
Motivation: Long-read assemblers face challenges in discerning closely related viral or bacterial strains, often collapsing similar strains into a single sequence. This limitation has been hampering metagenome analysis, as diverse strains may harbor crucial functional distinctions. Results: We intro...
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2024-10-01
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| Online Access: | https://peercommunityjournal.org/articles/10.24072/pcjournal.481/ |
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| author | Faure, Roland Lavenier, Dominique Flot, Jean-François |
| author_facet | Faure, Roland Lavenier, Dominique Flot, Jean-François |
| author_sort | Faure, Roland |
| collection | DOAJ |
| description | Motivation: Long-read assemblers face challenges in discerning closely related viral or bacterial strains, often collapsing similar strains into a single sequence. This limitation has been hampering metagenome analysis, as diverse strains may harbor crucial functional distinctions. Results: We introduce a novel software, HairSplitter, designed to retrieve strains from a partially or totally collapsed assembly and long reads. The method uses a custom variant-calling process to operate with erroneous long reads and introduces a new read binning algorithm to recover an a priori unknown number of strains. On noisy long reads, HairSplitter recovers more strains while being faster than state-of-the-art tools, both in the cases of viruses and bacteria. Availability: HairSplitter is freely available on GitHub at https://github.com/RolandFaure/Hairsplitter (https://doi.org/10.5281/zenodo.13753481). |
| format | Article |
| id | doaj-art-b81594132c7f42f18654488bc853851e |
| institution | Kabale University |
| issn | 2804-3871 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | Peer Community In |
| record_format | Article |
| series | Peer Community Journal |
| spelling | doaj-art-b81594132c7f42f18654488bc853851e2025-02-07T10:17:17ZengPeer Community InPeer Community Journal2804-38712024-10-01410.24072/pcjournal.48110.24072/pcjournal.481HairSplitter: haplotype assembly from long, noisy reads Faure, Roland0https://orcid.org/0000-0003-2245-4284Lavenier, Dominique1Flot, Jean-François2https://orcid.org/0000-0003-4091-7916Univ. Rennes, INRIA RBA, CNRS UMR 6074, Rennes, France; Service Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), Brussels, BelgiumUniv. Rennes, INRIA RBA, CNRS UMR 6074, Rennes, FranceService Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels -- (IB)2, Brussels, BelgiumMotivation: Long-read assemblers face challenges in discerning closely related viral or bacterial strains, often collapsing similar strains into a single sequence. This limitation has been hampering metagenome analysis, as diverse strains may harbor crucial functional distinctions. Results: We introduce a novel software, HairSplitter, designed to retrieve strains from a partially or totally collapsed assembly and long reads. The method uses a custom variant-calling process to operate with erroneous long reads and introduces a new read binning algorithm to recover an a priori unknown number of strains. On noisy long reads, HairSplitter recovers more strains while being faster than state-of-the-art tools, both in the cases of viruses and bacteria. Availability: HairSplitter is freely available on GitHub at https://github.com/RolandFaure/Hairsplitter (https://doi.org/10.5281/zenodo.13753481).https://peercommunityjournal.org/articles/10.24072/pcjournal.481/Metagenomes, Metaviromes, Haplotyping, Genome assembly, Strain separation |
| spellingShingle | Faure, Roland Lavenier, Dominique Flot, Jean-François HairSplitter: haplotype assembly from long, noisy reads Peer Community Journal Metagenomes, Metaviromes, Haplotyping, Genome assembly, Strain separation |
| title | HairSplitter: haplotype assembly from long, noisy reads
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| title_full | HairSplitter: haplotype assembly from long, noisy reads
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| title_fullStr | HairSplitter: haplotype assembly from long, noisy reads
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| title_full_unstemmed | HairSplitter: haplotype assembly from long, noisy reads
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| title_short | HairSplitter: haplotype assembly from long, noisy reads
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| title_sort | hairsplitter haplotype assembly from long noisy reads |
| topic | Metagenomes, Metaviromes, Haplotyping, Genome assembly, Strain separation |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.481/ |
| work_keys_str_mv | AT faureroland hairsplitterhaplotypeassemblyfromlongnoisyreads AT lavenierdominique hairsplitterhaplotypeassemblyfromlongnoisyreads AT flotjeanfrancois hairsplitterhaplotypeassemblyfromlongnoisyreads |