Skmer: assembly-free and alignment-free sample identification using genome skims
Abstract The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes co...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-02-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13059-019-1632-4 |
| _version_ | 1818109335677435904 |
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| author | Shahab Sarmashghi Kristine Bohmann M. Thomas P. Gilbert Vineet Bafna Siavash Mirarab |
| author_facet | Shahab Sarmashghi Kristine Bohmann M. Thomas P. Gilbert Vineet Bafna Siavash Mirarab |
| author_sort | Shahab Sarmashghi |
| collection | DOAJ |
| description | Abstract The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally. This approach discards the nuclear DNA, which constitutes the vast majority of the data. In contrast, we suggest using all unassembled reads. We introduce an assembly-free and alignment-free tool, Skmer, to compute genomic distances between the query and reference genome skims. Skmer shows excellent accuracy in estimating distances and identifying the closest match in reference datasets. |
| first_indexed | 2024-12-11T02:29:37Z |
| format | Article |
| id | doaj.art-b033993d37824b4bad6b7ae8537429df |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-11T02:29:37Z |
| publishDate | 2019-02-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-b033993d37824b4bad6b7ae8537429df2022-12-22T01:23:51ZengBMCGenome Biology1474-760X2019-02-0120112010.1186/s13059-019-1632-4Skmer: assembly-free and alignment-free sample identification using genome skimsShahab Sarmashghi0Kristine Bohmann1M. Thomas P. Gilbert2Vineet Bafna3Siavash Mirarab4Department of Electrical & Computer Engineering, University of CaliforniaEvolutionary Genomics, Natural History Museum of Denmark, University of CopenhagenEvolutionary Genomics, Natural History Museum of Denmark, University of CopenhagenDepartment of Computer Science & Engineering, University of CaliforniaDepartment of Electrical & Computer Engineering, University of CaliforniaAbstract The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally. This approach discards the nuclear DNA, which constitutes the vast majority of the data. In contrast, we suggest using all unassembled reads. We introduce an assembly-free and alignment-free tool, Skmer, to compute genomic distances between the query and reference genome skims. Skmer shows excellent accuracy in estimating distances and identifying the closest match in reference datasets.http://link.springer.com/article/10.1186/s13059-019-1632-4Assembly-freeAlignment-freeDNA BarcodingGenome skimmingDNA reference databaseSecond generation sequencing |
| spellingShingle | Shahab Sarmashghi Kristine Bohmann M. Thomas P. Gilbert Vineet Bafna Siavash Mirarab Skmer: assembly-free and alignment-free sample identification using genome skims Genome Biology Assembly-free Alignment-free DNA Barcoding Genome skimming DNA reference database Second generation sequencing |
| title | Skmer: assembly-free and alignment-free sample identification using genome skims |
| title_full | Skmer: assembly-free and alignment-free sample identification using genome skims |
| title_fullStr | Skmer: assembly-free and alignment-free sample identification using genome skims |
| title_full_unstemmed | Skmer: assembly-free and alignment-free sample identification using genome skims |
| title_short | Skmer: assembly-free and alignment-free sample identification using genome skims |
| title_sort | skmer assembly free and alignment free sample identification using genome skims |
| topic | Assembly-free Alignment-free DNA Barcoding Genome skimming DNA reference database Second generation sequencing |
| url | http://link.springer.com/article/10.1186/s13059-019-1632-4 |
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