Skmer: assembly-free and alignment-free sample identification using genome skims.
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ABSTRACT:
SUBMITTER: Sarmashghi S
PROVIDER: S-EPMC6374904 | biostudies-literature | 2019 Feb
REPOSITORIES: biostudies-literature
Publications
Skmer: assembly-free and alignment-free sample identification using genome skims.
Sarmashghi Shahab S Bohmann Kristine K P Gilbert M Thomas MT Bafna Vineet V Mirarab Siavash S
Genome biology 20190213 1
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 too ...[more]
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