Edena: very short reads assembler

Overview

Edena (Exact DE Novo Assembler) is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer. Edena is based on the traditional overlap layout paradigm. All exact overlaps between any pair of reads are computed and structured in a graph (overlap step). Basically, the reads are indexed in a prefix array and overlaps are revealed by dichotomic search in the arrays. The graph is then analyzed to remove transitive and spurious edges (layout step). Finally, contigs that can be assembled following unambiguous path in the graph are given as output. Edena allows to produce contigs of several kbp with a near full coverage of the bacterial genome being sequenced.

Reference

De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.
D. Hernandez, P. François, L. Farinelli, M. Osteras, and J. Schrenzel.
Genome Research. 18:802-809, 2008.

Download

Latest Edena version is 2.1.1 (March 17, 2008)
This release fixes a bug regarding the contig ends trimming.

Edena for Linux-32
Edena for Linux-64
Edena for Windows (experimental) This is a command line application.

Staphylococcus aureus strain MW2 reads dataset (this dataset is the one used in the publication):

mw2Reads.seq.gz (63Mo)

Announcement list

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Contact

Dr David HERNANDEZ