TL;DR
Ococo is a real-time, resource-efficient variant caller that infers single-nucleotide variants and consensus directly from streaming, unsorted read alignments, reducing computational costs compared to traditional methods.
Contribution
It introduces Ococo, the first tool capable of online variant calling from streaming alignments, enabling faster and more memory-efficient genomic analysis.
Findings
Operates in real-time during read streaming
Uses compact counters for memory efficiency
Suitable for resource-limited or progressive sequencing scenarios
Abstract
Motivation: Identifying genomic variants is an essential step for connecting genotype and phenotype. The usual approach consists of statistical inference of variants from alignments of sequencing reads. State-of-the-art variant callers can resolve a wide range of different variant types with high accuracy. However, they require that all read alignments be available from the beginning of variant calling and be sorted by coordinates. Sorting is computationally expensive, both memory- and speed-wise, and the resulting pipelines suffer from storing and retrieving large alignments files from external memory. Therefore, there is interest in developing methods for resource-efficient variant calling. Results: We present Ococo, the first program capable of inferring variants in a real-time, as read alignments are fed in. Ococo inputs unsorted alignments from a stream and infers…
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