LevioSAM: fast lift-over of variant-aware reference alignments | Zendy

Taher Mun | Zendy; Nae-Chyun Chen | Zendy; Ben Langmead | Zendy

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LevioSAM: fast lift-over of variant-aware reference alignments

Author(s) -

Taher Mun,

Nae-Chyun Chen,

Ben Langmead

Publication year - 2021

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btab396

Subject(s) - computer science , bottleneck , lift (data mining) , software , population , task (project management) , file format , data mining , programming language , embedded system , demography , management , sociology , economics

As more population genetics datasets and population-specific references become available, the task of translating ('lifting') read alignments from one reference coordinate system to another is becoming more common. Existing tools generally require a chain file, whereas VCF files are the more common way to represent variation. Existing tools also do not make effective use of threads, creating a post-alignment bottleneck.

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