GAPPadder: a sensitive approach for closing gaps on draft genomes with short sequence reads.

ABSTRACT:

Background

Closing gaps in draft genomes is an important post processing step in genome assembly. It leads to more complete genomes, which benefits downstream genome analysis such as annotation and genotyping. Several tools have been developed for gap closing. However, these tools don't fully utilize the information contained in the sequence data. For example, while it is known that many gaps are caused by genomic repeats, existing tools often ignore many sequence reads that originate from a repeat-related gap.

Results

We compare GAPPadder with GapCloser, GapFiller and Sealer on one bacterial genome, human chromosome 14 and the human whole genome with paired-end and mate-paired reads with both short and long insert sizes. Empirical results show that GAPPadder can close more

SUBMITTER: Chu C 

PROVIDER: S-EPMC6551238 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature