Combining de novo and reference-guided assembly with scaffold_builder.

ABSTRACT: Genome sequencing has become routine, however genome assembly still remains a challenge despite the computational advances in the last decade. In particular, the abundance of repeat elements in genomes makes it difficult to assemble them into a single complete sequence. Identical repeats shorter than the average read length can generally be assembled without issue. However, longer repeats such as ribosomal RNA operons cannot be accurately assembled using existing tools. The application Scaffold_builder was designed to generate scaffolds - super contigs of sequences joined by N-bases - based on the similarity to a closely related reference sequence. This is independent of mate-pair information and can be used complementarily for genome assembly, e.g. when mate-pairs are not available or hav

SUBMITTER: Silva GG 

PROVIDER: S-EPMC4177539 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature