CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes.

ABSTRACT:

Background

Easy-to-use and fast bioinformatics pipelines for long-read assembly that go beyond the contig level to generate highly continuous chromosome-scale genomes from raw data remain scarce.

Result

Chromosome-Scale Assembler (CSA) is a novel computationally highly efficient bioinformatics pipeline that fills this gap. CSA integrates information from scaffolded assemblies (e.g., Hi-C or 10X Genomics) or even from diverged reference genomes into the assembly process. As CSA performs automated assembly of chromosome-sized scaffolds, we benchmark its performance against state-of-the-art reference genomes, i.e., conventionally built in a laborious fashion using multiple separate assembly tools and manual curation. CSA increases the contig lengths using scaffolding, local re-

SUBMITTER: Kuhl H 

PROVIDER: S-EPMC7247394 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature