Measuring, visualizing and diagnosing reference bias with biastools.
Ontology highlight
ABSTRACT:
SUBMITTER: Lin MJ
PROVIDER: S-EPMC10515925 | biostudies-literature | 2024 Feb
REPOSITORIES: biostudies-literature
Publications
Measuring, visualizing and diagnosing reference bias with biastools.
Lin Mao-Jan MJ Iyer Sheila S Chen Nae-Chyun NC Langmead Ben B
bioRxiv : the preprint server for biology 20240215
Many bioinformatics methods seek to reduce reference bias, but no methods exist to comprehensively measure it. Biastools analyzes and categorizes instances of reference bias. It works in various scenarios, i.e. (a) when the donor's variants are known and reads are simulated, (b) when donor variants are known and reads are real, and (c) when variants are unknown and reads are real. Using biastools, we observe that more inclusive graph genomes result in fewer biased sites. We find that end-to-end ...[more]
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