GapPredict - A Language Model for Resolving Gaps in Draft Genome Assemblies.

ABSTRACT: Short-read DNA sequencing instruments can yield over 10¹² bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using short reads due to both repetitive and difficult-to-sequence regions in these genomes. Some of the short read assembly challenges are mitigated by scaffolding assembled sequences using paired-end reads. However, unresolved sequences in these scaffolds appear as "gaps". Here, we introduce GapPredict - An implementation of a proof of concept that uses a character-level language model to predict unresolved nucleotides in scaffold gaps. We benchmarked GapPredict against the state-of-the-art gap-filling tool Sealer, and observed that the former can

SUBMITTER: Chen E 

PROVIDER: S-EPMC8772386 | biostudies-literature | 2021 Nov-Dec

REPOSITORIES: biostudies-literature