J Genomics 2014; 2:89-93. doi:10.7150/jgen.7298 This volume

Research Paper

Enly: Improving Draft Genomes through Reads Recycling

Marco Fondi1✉, Valerio Orlandini1, Giorgio Corti2, Marco Severgnini2, Marco Galardini1, Alessandro Pietrelli2, Fabio Fuligni2, Michele Iacono2, Ermanno Rizzi2, Gianluca De Bellis2, Renato Fani1

1. Dept. of Evolutionary Biology, Via Madonna del Piano 6, 50143 Sesto Fiorentino,Florence, Italy;
2. Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate (MI), Italy.

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Fondi M, Orlandini V, Corti G, Severgnini M, Galardini M, Pietrelli A, Fuligni F, Iacono M, Rizzi E, De Bellis G, Fani R. Enly: Improving Draft Genomes through Reads Recycling. J Genomics 2014; 2:89-93. doi:10.7150/jgen.7298. Available from https://www.jgenomics.com/v02p0089.htm

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The reconstruction of the complete genome sequence of an organism is an important point for comparative, functional and evolutionary genomics. Nevertheless, overcoming the problems encountered while completing the sequence of an entire genome can still be demanding in terms of time and resources. We have developed Enly, a simple tool based on the iterative mapping of sequence reads at contig edges, capable to extend the genomic contigs deriving from high-throughput sequencing, especially those deriving by Newbler-like assemblies. Testing it on a set of de novo draft genomes led to the closure of up to 20% of the gaps originally present. Enly is cross-platform and most of the steps of its pipeline are parallelizable, making easy and fast to improve a draft genome resulting from a de novo assembly.

Keywords: Genome assembly, Next Generation Sequencing, Contig extension, Newbler, 454.