Using long and linked reads to improve an Atlantic herring (Clupea harengus) genome assembly.

ABSTRACT: Atlantic herring (Clupea harengus) is one of the most abundant fish species in the world. It is an important economical and nutritional resource, as well as a crucial part of the North Atlantic ecosystem. In 2016, a draft herring genome assembly was published. Being a species of such importance, we sought to independently verify and potentially improve the herring genome assembly. We sequenced the herring genome generating paired-end, mate-pair, linked and long reads. Three assembly versions of the herring genome were generated based on a de novo assembly (A1), which was scaffolded using linked and long reads (A2) and then merged with the previously published assembly (A3). The resulting assemblies were compared using parameters describing the size, fragmentation, correctness, and complete

SUBMITTER: I Kongsstovu S 

PROVIDER: S-EPMC6881392 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature