Aggressive assembly of pyrosequencing reads with mates

By Jason Rafe Miller, Arthur L. Delcher, Sergey Koren, E. Venter, Brian Walenz, Anushka Brownley, Justin Johnson, Kelvin Li, C. Mobarry, Granger G. Sutton. Bioinform., 2008

574 citations recorded by the source corpus.

Motivation: DNA sequence reads from Sanger and pyrosequencing platforms differ in cost, accuracy, typical coverage, average read length and the variety of available paired-end protocols. Both read types can complement one another in a ‘hybrid’ approach to whole-genome shotgun sequencing projects, but assembly software must be modified to accommodate their different characteristics. This is true even of pyrosequencing mated and unmated read combinations. Without special modifications, assemblers tuned for homogeneous sequence data may perform poorly on hybrid data. Results: Celera Assembler was modified for combinations of ABI 3730 and 454 FLX reads. The revised pipeline called CABOG (Celera Assembler with the Best Overlap Graph) is robust to homopolymer run length uncertainty, high read coverage and heterogeneous read lengths. In tests on four genomes, it generated the longest contigs among all assemblers tested. It exploited the mate constraints provided by paired-end reads from either platform to build larger contigs and scaffolds, which were validated by comparison to a finished reference sequence. A low rate of contig mis-assembly was detected in some CABOG assemblies, but this was reduced in the presence of sufficient mate pair data. Availability: The software is freely available as open-source from http://wgs-assembler.sf.net under the GNU Public License. Contact: jmiller@jcvi.org Supplementary information: Supplementary data are available at Bioinformatics online.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/af508bba6447680641fa0649525a7fc5edbcea48

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In Molecular Biology

Citations in the corpus

GAGE: A critical evaluation of genome assemblies and assembly algorithms. (2012, unknown): “• CABOG (Miller et al. 2008) • MSR-CA (http://www.”
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads (2020, methodology): “Our approach is similar to run-length encoding (RLE), which has been previously applied to 454 (Miller et al. 2008), PacBio CLR (Li 2016, 2018; Ruan and Li 2020), and Oxford Nanopore (Shafin et al. 2020) reads.”
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. (2015, background): “Support has been subsequently added for 454 [78] and long reads [34 ].”
Oxford Nanopore MinION Sequencing and Genome Assembly (2016, background): “Typical examples of hybrid assem-blers are ALLPATHS-LG [51], Celera Assembler’s PacBio corrected reads pipeline (pacBioToCA [52]), SPAdes [53], and SSPACE-LongRead [32].”
Assembly of long, error-prone reads using repeat graphs (2018, background): “Developers of OLC approaches realized the importance of repeat characterization and attempted to improve the best overlap graph (BOG) representation (Miller et al., 2008) by developing the OLC-based Bogart graph for representing repeats (Koren et al.”
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies (2020, methodology): “Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler [43] and has since been migrated and maintained as part of Canu [33].”
Assembly Algorithms for Next-Generation Sequencing Data (2010, unknown): “The Celera Assembler [37] is a Sanger-era OLC assembler revised for 454 data [46].”
Hybrid error correction and de novo assembly of single-molecule sequencing reads (2012, methodology): “( a ) Effect of PacBio corrected read (PBcR) length on contig size is measured for the OLC assembler Celera Assembler 11 and the de Brujin assembler SOAPdenovo 49 .”