Journal
BIOINFORMATICS
Volume 34, Issue 24, Pages 4293-4296Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/bty548
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Funding
- University of Arkansas Endowments (Bruker Professorship in Life Sciences)
- University of Arkansas Endowments (21st Century Chair in Global Climate Change Biology)
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Motivation: It is a non-trivial task to identify and design capture probes ('baits') for the diverse array of targeted-enrichment methods now available (e.g. ultra-conserved elements, anchored hybrid enrichment, RAD-capture). This often involves parsing large genomic alignments, followed by multiple steps of curating candidate genomic regions to optimize targeted information content (e.g. genetic variation) and to minimize potential probe dimerization and non-target enrichment. Results: In this context, we developed MrBait, a user-friendly, generalized software pipeline for identification, design and optimization of targeted-enrichment probes across a range of target-capture paradigms. MrBait is an open-source codebase that leverages native parallelization capabilities in Python and mitigates memory usage via a relational-database back-end. Numerous filtering methods allow comprehensive optimization of designed probes, including built-in functionality that employs BLAST, similarity-based clustering and a graph-based algorithm that 'rescues' failed probes.
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