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% of the reference human genome. Analysis of these contigs identified polymorphic and novel sequences not present in the human reference assembly, which were validated by alignment to alternate human assemblies and to other primate genomes.

References in zbMATH (referenced in 13 articles )

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  1. Chikhi, Rayan: A tale of optimizing the space taken by de Bruijn graphs (2021)
  2. Acuña, V.; Grossi, R.; Italiano, G. F.; Lima, L.; Rizzi, R.; Sacomoto, G.; Sagot, M.-F.; Sinaimeri, B.: On bubble generators in directed graphs (2020)
  3. Pan, Weihua; Jiang, Tao; Lonardi, Stefano: OMGS: optical map-based genome scaffolding (2019)
  4. Ryšavý, Petr; Železný, Filip: Estimating sequence similarity from read sets for clustering next-generation sequencing data (2019)
  5. Wright, Christopher; Krishnamoorty, Sriram; Kulkarni, Milind: MULKSG: \textitMULtiple\textitK\textitSimultaneous\textitGraphassembly (2019)
  6. Alipanahi, Bahar; Salmela, Leena; Puglisi, Simon J.; Muggli, Martin; Boucher, Christina: Disentangled long-read de Bruijn graphs via optical maps (2017)
  7. Bonizzoni, Paola; Della Vedova, Gianluca; Pirola, Yuri; Previtali, Marco; Rizzi, Raffaella: An external-memory algorithm for string graph construction (2017)
  8. Jean, Géraldine; Radulescu, Andreea; Rusu, Irena: The contig assembly problem and its algorithmic solutions (2017)
  9. Liu, Yongchao; Schmidt, Bertil: CUSHAW suite: parallel and efficient algorithms for NGS read alignment (2017)
  10. Axelson-Fisk, Marina: Comparative gene finding. Models, algorithms and implementation (2015)
  11. Sergushichev, A. A.; Aleksandrov, A. V.; Kazakov, S. V.; Tsarev, F. N.; Shalyto, A. A.: Combining de Bruijn graphs, overlap graphs and microassembly for \textitdenovo genome assembly (2013)
  12. Rodríguez-Ezpeleta, Naiara (ed.); Hackenberg, Michael (ed.); Aransay, Ana M. (ed.): Bioinformatics for high throughput sequencing (2012)
  13. Díaz, David; Esteban, Francisco José; Hernández, Pilar; Caballero, Juan Antonio; Dorado, Gabriel; Gálvez, Sergio: Parallelizing and optimizing a bioinformatics pairwise sequence alignment algorithm for many-core architecture (2011) ioport