ARACHNE: a whole-genome shotgun assembler.

By Serafim Batzoglou, David B. Jaffe, Ken Stanley, Jonathan Butler, S. Gnerre, E. Mauceli, Bonnie Berger, Jill P. Mesirov, Eric S. Lander. Genome Research, 2002

690 citations recorded by the source corpus.

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% coverage with an N50 contig length of 324 kb and an N50 supercontig length of 5143 kb. The assembly accuracy was high, although not perfect: small errors occurred at a frequency of roughly 1 per 1 Mb (typically, deletion of approximately 1 kb in size), with a very small number of other misassemblies. The assembly was rapid: the Drosophila assembly required only 21 hours on a single 667 MHz processor and used 8.4 Gb of memory.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/88bfc94ad402b8bfd624c7d2691ec9012fd2f5ed

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Citations in the corpus

De novo assembly of haplotype-resolved genomes with trio binning (2018, neutral): “11 and 12).”
Genomics of the fungal kingdom: Insights into eukaryotic biology (2005, background): “Advances in assembly algorithms (Myers et al. 2000; Aparicio et al. 2002; Batzoglou et al. 2002; Jaffe et al. 2003; Mullikin and Ning 2003) and the inclusion of end sequences from large insert clones (e.”
Assembly Algorithms for Next-Generation Sequencing Data (2010, neutral): “It was optimized for large genomes in software including Celera Assembler [37], Arachne [38] [39], and CAP and PCAP [40].”
Assembly of large genomes using second-generation sequencing. (2010, background): “This can work well, although overlap graph assemblers (CABOG and ARACHNE) are more mature than the new short read assemblers and generally produce much better assemblies, especially due to their more sophisticated use of mate pairs.”
Short read fragment assembly of bacterial genomes. (2008, methodology): “2003), or by clustering and aligning reads prior to assembly (Batzoglou et al. 2002). In HTSR sequencing, constructing multiple alignments of short reads is very time consuming, and so we correct errors in reads prior to assembly using a method called spectral alignment (SA) that does not use a mult”
Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies (2010, methodology): “In contrast, the Roche/454 system allows the incorporation of all nucleotides of a homopolymer during the same cycle.”
Sequencing and comparison of yeast species to identify genes and regulatory elements (2003, methodology): “The information was then assembled with the Arachne computer progra”
Versatile and open software for comparing large genomes (2004, background): “The explosion of genome sequencing has brought with it an explosion in genome-assembly programs, with several new assemblers either under development or recently released [10-12].”
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology (2012, methodology): “Initially, assembly methods used relatively long (500– 800 bp) shotgun Sanger reads with Overlap-Layout-Consensus assemblers [6–11].”
A Bioinformatician's Guide to Metagenomics (2008, background): “A variety of assembly programs are publicly available, including Phrap (www.phrap.org), Arachne (13, 65), the Celera Assembler (97), PGA (http://www.paracel.com/), and CAP3 (60; for a description and history of these assemblers, we refer the reader to reference 79).”