Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage
Abstract Background In many fields of biomedical research, it is important to estimate phylogenetic distances between taxa based on low-coverage sequencing reads. Major applications are, for example, phylogeny reconstruction, species identification from small sequencing samples, or bacterial strain...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-12-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-019-3205-7 |
| _version_ | 1818920990994857984 |
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| author | Anna-Katharina Lau Svenja Dörrer Chris-André Leimeister Christoph Bleidorn Burkhard Morgenstern |
| author_facet | Anna-Katharina Lau Svenja Dörrer Chris-André Leimeister Christoph Bleidorn Burkhard Morgenstern |
| author_sort | Anna-Katharina Lau |
| collection | DOAJ |
| description | Abstract Background In many fields of biomedical research, it is important to estimate phylogenetic distances between taxa based on low-coverage sequencing reads. Major applications are, for example, phylogeny reconstruction, species identification from small sequencing samples, or bacterial strain typing in medical diagnostics. Results We adapted our previously developed software program Filtered Spaced-Word Matches (FSWM) for alignment-free phylogeny reconstruction to take unassembled reads as input; we call this implementation Read-SpaM. Conclusions Test runs on simulated reads from semi-artificial and real-world bacterial genomes show that our approach can estimate phylogenetic distances with high accuracy, even for large evolutionary distances and for very low sequencing coverage. |
| first_indexed | 2024-12-20T01:30:32Z |
| format | Article |
| id | doaj.art-607e02c3582e48a59e71f08bd4a4a446 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-20T01:30:32Z |
| publishDate | 2019-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-607e02c3582e48a59e71f08bd4a4a4462022-12-21T19:58:08ZengBMCBMC Bioinformatics1471-21052019-12-0120S2011510.1186/s12859-019-3205-7Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverageAnna-Katharina Lau0Svenja Dörrer1Chris-André Leimeister2Christoph Bleidorn3Burkhard Morgenstern4Universität Göttingen, Department of BioinformaticsUniversität Göttingen, Department of BioinformaticsUniversität Göttingen, Department of BioinformaticsUniversität Göttingen, Department of Animal Evolution and BiodiversityUniversität Göttingen, Department of BioinformaticsAbstract Background In many fields of biomedical research, it is important to estimate phylogenetic distances between taxa based on low-coverage sequencing reads. Major applications are, for example, phylogeny reconstruction, species identification from small sequencing samples, or bacterial strain typing in medical diagnostics. Results We adapted our previously developed software program Filtered Spaced-Word Matches (FSWM) for alignment-free phylogeny reconstruction to take unassembled reads as input; we call this implementation Read-SpaM. Conclusions Test runs on simulated reads from semi-artificial and real-world bacterial genomes show that our approach can estimate phylogenetic distances with high accuracy, even for large evolutionary distances and for very low sequencing coverage.https://doi.org/10.1186/s12859-019-3205-7Alignment-freePhylogenomicsUnassembled reads |
| spellingShingle | Anna-Katharina Lau Svenja Dörrer Chris-André Leimeister Christoph Bleidorn Burkhard Morgenstern Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage BMC Bioinformatics Alignment-free Phylogenomics Unassembled reads |
| title | Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage |
| title_full | Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage |
| title_fullStr | Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage |
| title_full_unstemmed | Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage |
| title_short | Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage |
| title_sort | read spam assembly free and alignment free comparison of bacterial genomes with low sequencing coverage |
| topic | Alignment-free Phylogenomics Unassembled reads |
| url | https://doi.org/10.1186/s12859-019-3205-7 |
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