title: Enly: Improving Draft Genomes through Reads Recycling.
abstract: 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.
authors.affiliation: 1. Dept. of Evolutionary Biology, Via Madonna del Piano 6, 50143 Sesto Fiorentino,Florence, Italy;
authors.forename: Marco
authors.initials: M
authors.lastname: Fondi
authors.affiliation: 1. Dept. of Evolutionary Biology, Via Madonna del Piano 6, 50143 Sesto Fiorentino,Florence, Italy;
authors.forename: Valerio
authors.initials: V
authors.lastname: Orlandini
authors.affiliation: 2. Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate (MI), Italy.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Corti
authors.affiliation: 2. Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate (MI), Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Severgnini
authors.affiliation: 1. Dept. of Evolutionary Biology, Via Madonna del Piano 6, 50143 Sesto Fiorentino,Florence, Italy;
authors.forename: Marco
authors.initials: M
authors.lastname: Galardini
authors.affiliation: 2. Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate (MI), Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Pietrelli
authors.affiliation: 2. Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate (MI), Italy.
authors.forename: Fabio
authors.initials: F
authors.lastname: Fuligni
authors.affiliation: 2. Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate (MI), Italy.
authors.forename: Michele
authors.initials: M
authors.lastname: Iacono
authors.affiliation: 2. Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate (MI), Italy.
authors.forename: Ermanno
authors.initials: E
authors.lastname: Rizzi
authors.affiliation: 2. Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate (MI), Italy.
authors.forename: Gianluca
authors.initials: G
authors.lastname: De Bellis
authors.affiliation: 1. Dept. of Evolutionary Biology, Via Madonna del Piano 6, 50143 Sesto Fiorentino,Florence, Italy;
authors.forename: Renato
authors.initials: R
authors.lastname: Fani
keywords: 454.; Contig extension; Genome assembly; Newbler; Next Generation Sequencing