ABySS: a parallel assembler for short read sequence data.

By Jared T Simpson, Kim G. Wong, Shaun D. Jackman, Jacqueline E. Schein, Steven J. M. Jones, Inanç Birol. Genome Research, 2009

1,394 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6782425b8f6589045104c1065d2fd2d6a008b3d1

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Citations in the corpus

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information (2014, methodology): “The aim is to combine the short sequencing reads into a minimum number of linear stretches, though this goal is only partially achieved by draft assembly methods such as Velvet [1], SOAPdenovo [2] or ABySS [3].”
Efficient de novo assembly of large genomes using compressed data structures. (2012, methodology): “Currently available assemblers require either a single computer with very large amounts of memory—typically in the hundreds of gigabytes (Li et al. 2010b; Gnerre et al. 2011)—or a large distributed cluster of tightly coupled computers (Simpson et al. 2009; Boisvert et al. 2010).”
Genome assembly reborn: recent computational challenges (2009, background): “De novo assembly of these data has largely been restricted to bacterial genomes, though an assembly of an entire human genome from Solexa reads was recently reported [22].”
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels (2012, neutral): “Received on December 2, 2011; revised on January 20, 2012; accepted on February 17, 2012”
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads (2011, positive): “Given a set of sequence reads, the de Bruijn graph based assemblers [16, 27, 12, 21] ﬁrst break each read into k -mers (words of length k ).”
Circos: an information aesthetic for comparative genomics. (2009, methodology): “Individual BACs identified to capture rearrangements were subject to short-read Illumina sequencing and assembled with ABySS (Simpson et al. 2009).”
Redundans: an assembly pipeline for highly heterozygous genomes (2015, neutral): “On the other hand, the assemblies reconstructed for simulated genomes with a higher level of LOH had fewer full size chromosomes (1,2), if any.”
An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis (2013, neutral): “4 [19] with default parameters except: k=71, b=1000, p=0.”
Computational solutions for omics data (2013, background): “Recently, several crucial evaluations of numerous popular genome assemblers, including de Bruijn-graph-based 21–24 and FM-index-based (see BOX 2 and ‘Read mapping in next-generation sequencing’) assemblers 26 , have been carried out on four genomes with a wide phylogenetic range and varying degrees…”
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data (2011, background): “Contact: artemis@sanger.ac.uk; tjc@sanger.ac.uk Received on September 6, 2011; revised on November 10, 2011; accepted on December 17, 2011”
Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach (2013, result): “3 (26) to further verify the results obtained by MITObim.”