ABySS swMATH ID: 17343 Software Authors: Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J., Birol, I. Description: ABySS: a parallel assembler for short read sequence data. Widespread adoption of massively parallel deoxyribonucleic acid (DNA) sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the available tools is their inability to efficiently assemble vast amounts of data generated from large-scale sequencing projects, such as the sequencing of individual human genomes to catalog natural genetic variation. To address this limitation, we developed ABySS (Assembly By Short Sequences), a parallelized sequence assembler. As a demonstration of the capability of our software, we assembled 3.5 billion paired-end reads from the genome of an African male publicly released by Illumina, Inc. Approximately 2.76 million contigs ≥100 base pairs (bp) in length were created with an N50 size of 1499 bp, representing 68 Homepage: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694472/ Related Software: Velvet; SPAdes; SOAPdenovo; IDBA-UD; GAGE; ALLPATHS; ARACHNE; IDBA; MEGAHIT; ART; SSAKE; SHARCGS; QSRA; Meta-IDBA; SHRiMP; GATK; QUAST; GitHub; CAP3; BLAT Cited in: 12 Publications all top 5 Cited by 40 Authors 1 Acuña, Vicente 1 Aleksandrov, A. V. 1 Alipanahi, Bahar 1 Aransay, Ana M. 1 Axelson-Fisk, Marina 1 Bonizzoni, Paola 1 Boucher, Christina 1 Chikhi, Rayan 1 Della Vedova, Gianluca 1 Grossi, Roberto 1 Hackenberg, Michael 1 Italiano, Giuseppe Francesco 1 Jean, Géraldine 1 Jiang, Tao 1 Kazakov, S. V. 1 Krishnamoorty, Sriram 1 Kulkarni, Milind Narayanrao 1 Liu, Yongchao 1 Lonardi, Stefano 1 Muggli, Martin D. 1 Pan, Weihua 1 Pirola, Yuri 1 Previtali, Marco 1 Puglisi, Simon J. 1 Radulescu, Andreea 1 Rizzi, Raffaella 1 Rizzi, Romeo 1 Rodríguez-Ezpeleta, Naiara 1 Rusu, Irena 1 Ryšavý, Petr 1 Sacomoto, Gustavo 1 Sagot, Marie-France 1 Salmela, Leena 1 Schmidt, Bertil 1 Sergushichev, Alexey A. 1 Shalyto, A. A. 1 Sinaimeri, Blerina 1 Tsarev, F. N. 1 Wright, Christopher 1 Železný, Filip Cited in 4 Serials 2 Algorithmica 1 Data Mining and Knowledge Discovery 1 Computational Biology 1 Izvestiya Saratovskogo Universiteta. Novaya Seriya. Seriya Matematika, Mekhanika, Informatika all top 5 Cited in 7 Fields 10 Biology and other natural sciences (92-XX) 6 Computer science (68-XX) 3 Combinatorics (05-XX) 2 Operations research, mathematical programming (90-XX) 1 General and overarching topics; collections (00-XX) 1 Probability theory and stochastic processes (60-XX) 1 Statistics (62-XX) Citations by Year