swMATH ID: 7552
Software Authors: Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES
Description: ARACHNE: a whole-genome shotgun assembler. We describe a new computer system, called ARACHNE, for assembling genome sequence using paired-end whole-genome shotgun reads. ARACHNE has several key features, including an efficient and sensitive procedure for finding read overlaps, a procedure for scoring overlaps that achieves high accuracy by correcting errors before assembly, read merger based on forward-reverse links, and detection of repeat contigs by forward-reverse link inconsistency. To test ARACHNE, we created simulated reads providing approximately 10-fold coverage of the genomes of H. influenzae, S. cerevisiae, and D. melanogaster, as well as human chromosomes 21 and 22. The assemblies of these simulated reads yielded nearly complete coverage of the respective genomes, with a small number of contigs joined into a smaller number of supercontigs (or scaffolds). For example, analysis of the D. melanogaster genome yielded approximately 98
Homepage: http://www.ncbi.nlm.nih.gov/pubmed/11779843
Related Software: Velvet; ABySS; CAP3; BLAT; SHARCGS; ALLPATHS; IDBA-UD; SOAPdenovo; GAGE; RePS; RepeatMasker; C4.5; Phusion; MULKSG; MEGAHIT; GitHub; QUAST; SPAdes; Python; Oases
Cited in: 6 Publications

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