High-fidelity (repeat) consensus sequences from short reads using combined read clustering and assembly.

ABSTRACT:

Background

Despite the many cheap and fast ways to generate genomic data, good and exact genome assembly is still a problem, with especially the repeats being vastly underrepresented and often misassembled. As short reads in low coverage are already sufficient to represent the repeat landscape of any given genome, many read cluster algorithms were brought forward that provide repeat identification and classification. But how can trustworthy, reliable and representative repeat consensuses be derived from unassembled genomes?

Results

Here, we combine methods from repeat identification and genome assembly to derive these robust consensuses. We test several use cases, such as (1) consensus building from clustered short reads of non-model genomes, (2) from genome-wide amplificati

SUBMITTER: Mann L 

PROVIDER: S-EPMC10809544 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature