An Eulerian path approach to DNA fragment assembly

By Pavel A. Pevzner, Haixu Tang, Michael S. Waterman. Proceedings of the National Academy of Sciences of the United States of America, 2001

1,463 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c9284fd6a3bb033bf5e21a2fc512dd2be958bfad

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Citations in the corpus

PCAP: a whole-genome assembly program. (2003, background): “…assembly programs (Staden 1980; Peltola et al. 1984; Huang 1992; Green 1995; Kececioglu and Myers 1995; Sut-ton et al. 1995; Huang and Madan 1999; Kim and Segre 1999; Chen and Skiena 2000; Pevzner et al. 2001) The existing programs have made WGS successful in several genome sequencing projects .”
Hive plots - rational approach to visualizing networks (2012, neutral): “disease [9], genome assembly [10, 11] and classifying”
Sequence assembly demystified (2013, methodology): “Many of the techniques developed in Euler have been emulated and extended by most modern de Bruijn graph assemblers.”
Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery (2010, methodology): “As a result, most de novo assemblers for short reads utilize a different algorithm, based on the de Bruijn graph approach (Pevzner et al. 2001), in which reads are sorted into words of k-nucleotides, or k-mers, and mapped through a graph, going from one word to the next in a determined order.”
A window into third-generation sequencing. (2010, methodology): “A number of assemblers for de novo assembly have been written for SGS, including overlap graph approaches in which contigs are assembled by looking at sequence overlaps, like Edna (46), VCAKE (47) and SHARCGS (48); those based on the de Bruijn graph data structure (49), like Velvet (50), EULER-SR (5”
A Primer on Metagenomics (2010, methodology): “The EULER assembler [49,50] was the first to present this technique using de Bruijn graphs.”
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. (2015, result): “[64], is to find a path through the de Bruijn graph that is consistent with the sequencing reads.”
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly (2012, methodology): “mended by mapping reads back to the graph and bisecting repeats shorter than the reads, a procedure some called as read threading. Many de Buijn graph based assemblers essentially take this strategy (Pevzner et al., 2001; Chaisson et al., 2009; Zerbino et al., 2009; Li et al., 2010), though they may”