ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.

ABSTRACT:

Background

The long-range sequencing information captured by linked reads, such as those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields accurate and contiguous draft genome assemblies. We introduce ARKS, an alignment-free linked read genome scaffolding methodology that uses linked reads to organize genome assemblies further into contiguous drafts. Our approach departs from other read alignment-dependent linked read scaffolders, including our own (ARCS), and uses a kmer-based mapping approach. The kmer mapping strategy has several advantages over read alignment methods, including better usability and faster processing, as it precludes the need for input sequence formatting and draft sequence assembly indexing. The reliance on kmers instead of r

SUBMITTER: Coombe L 

PROVIDER: S-EPMC6011487 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature