FGAP: an automated gap closing tool.

ABSTRACT:

Background

The fast reduction of prices of DNA sequencing allowed rapid accumulation of genome data. However, the process of obtaining complete genome sequences is still very time consuming and labor demanding. In addition, data produced from various sequencing technologies or alternative assemblies remain underexplored to improve assembly of incomplete genome sequences.

Findings

We have developed FGAP, a tool for closing gaps of draft genome sequences that takes advantage of different datasets. FGAP uses BLAST to align multiple contigs against a draft genome assembly aiming to find sequences that overlap gaps. The algorithm selects the best sequence to fill and eliminate the gap.

Conclusions

FGAP reduced the number of gaps by 78% in an E. coli draft genome assembly u

SUBMITTER: Piro VC 

PROVIDER: S-EPMC4091766 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature