FGAP: an automated gap closing tool

BMC Research Notes

Roberto T Raittz¹  Emanuel M Souza²  Fabio O Pedrosa²  Maria BR Steffens²  Vinicius A Weiss²  Helisson Faoro²  Vitor C Piro¹ 

[1] Laboratory of Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, PR, Brazil, Rua Dr. Alcides Vieira Arcoverde 1225, Curitiba, Paraná, Brazil;Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, PR, Brazil, Av. Cel. Francisco H. dos Santos, Curitiba, Paraná, Brazil

关键词: Gap closure;    Gap filling;    Genome finishing;   

Others  :  1132468
DOI  :  10.1186/1756-0500-7-371

 received in 2014-02-27, accepted in 2014-06-09,  发布年份 2014

【 摘 要 】

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 using two different sequencing technologies, Illumina and 454. Using PacBio long reads, 98% of gaps were solved. In human chromosome 14 assemblies, FGAP reduced the number of gaps by 35%. All the inserted sequences were validated with a reference genome using QUAST. The source code and a web tool are available at http://www.bioinfo.ufpr.br/fgap/ webcite.

【 授权许可】

   
2014 Piro et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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