LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads.

ABSTRACT:

Background

Owing to the complexity of the assembly problem, we do not yet have complete genome sequences. The difficulty in assembling reads into finished genomes is exacerbated by sequence repeats and the inability of short reads to capture sufficient genomic information to resolve those problematic regions. In this regard, established and emerging long read technologies show great promise, but their current associated higher error rates typically require computational base correction and/or additional bioinformatics pre-processing before they can be of value.

Results

We present LINKS, the Long Interval Nucleotide K-mer Scaffolder algorithm, a method that makes use of the sequence properties of nanopore sequence data and other error-containing sequence data, to scaffold hig

SUBMITTER: Warren RL 

PROVIDER: S-EPMC4524009 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature