Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2008 Dec 15;24(24):2818-24.
doi: 10.1093/bioinformatics/btn548. Epub 2008 Oct 24.

Aggressive assembly of pyrosequencing reads with mates

Jason R Miller  1 , Arthur L Delcher, Sergey Koren, Eli Venter, Brian P Walenz, Anushka Brownley, Justin Johnson, Kelvin Li, Clark Mobarry, Granger Sutton
Affiliations

Aggressive assembly of pyrosequencing reads with mates

Jason R Miller et al. Bioinformatics. .

Abstract

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.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Two representations of a best overlap graph. In (a), the layout resembles a multiple sequence alignment. In (b) each read is represented by two nodes joined by an undirected edge. Arrows represent best overlaps, where best means covering the most sequence. There are mutual best overlaps between successive pairs of reads A through D. Due to erroneous bases at one end (wavy line), read E has a non-mutual best overlap to B. Paths span undirected and directed edges alternately. Path EBA converges on path ABCD. CABOG scores read E lower than the others since only three reads are on paths from it. Starting with any one of the high-scoring reads, CABOG would build initial unitig ABCD, then E. Using saved information about each path intersection, CABOG would discount the intersection at B because the path from E spanned only one read before B. It would break ABCD only if there were also a change in read arrival rate at B, which is not the case here. Although linear-time directed-path following finds the longest possible unitig in this constructed case, it is not guaranteed to do so when paths span multiple intersections.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

  • Molecular epidemiologic investigation of an anthrax outbreak among heroin users, Europe.
    Price EP, Seymour ML, Sarovich DS, Latham J, Wolken SR, Mason J, Vincent G, Drees KP, Beckstrom-Sternberg SM, Phillippy AM, Koren S, Okinaka RT, Chung WK, Schupp JM, Wagner DM, Vipond R, Foster JT, Bergman NH, Burans J, Pearson T, Brooks T, Keim P. Price EP, et al. Emerg Infect Dis. 2012 Aug;18(8):1307-13. doi: 10.3201/eid1808.111343. Emerg Infect Dis. 2012. PMID: 22840345 Free PMC article.
  • Unbiased approach for virus detection in skin lesions.
    Bzhalava D, Johansson H, Ekström J, Faust H, Möller B, Eklund C, Nordin P, Stenquist B, Paoli J, Persson B, Forslund O, Dillner J. Bzhalava D, et al. PLoS One. 2013 Jun 28;8(6):e65953. doi: 10.1371/journal.pone.0065953. Print 2013. PLoS One. 2013. PMID: 23840382 Free PMC article.
  • Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction.
    Laehnemann D, Borkhardt A, McHardy AC. Laehnemann D, et al. Brief Bioinform. 2016 Jan;17(1):154-79. doi: 10.1093/bib/bbv029. Epub 2015 May 29. Brief Bioinform. 2016. PMID: 26026159 Free PMC article.
  • Genome sequence of the model medicinal mushroom Ganoderma lucidum.
    Chen S, Xu J, Liu C, Zhu Y, Nelson DR, Zhou S, Li C, Wang L, Guo X, Sun Y, Luo H, Li Y, Song J, Henrissat B, Levasseur A, Qian J, Li J, Luo X, Shi L, He L, Xiang L, Xu X, Niu Y, Li Q, Han MV, Yan H, Zhang J, Chen H, Lv A, Wang Z, Liu M, Schwartz DC, Sun C. Chen S, et al. Nat Commun. 2012 Jun 26;3:913. doi: 10.1038/ncomms1923. Nat Commun. 2012. PMID: 22735441 Free PMC article.
  • HASLR: Fast Hybrid Assembly of Long Reads.
    Haghshenas E, Asghari H, Stoye J, Chauve C, Hach F. Haghshenas E, et al. iScience. 2020 Aug 21;23(8):101389. doi: 10.1016/j.isci.2020.101389. Epub 2020 Jul 25. iScience. 2020. PMID: 32781410 Free PMC article.
See all "Cited by" articles

References

    1. Bentley DR. Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 2006;16:545–552. - PubMed
    1. Blattner FR, et al. The complete genome sequence of Escherichia coli K-12. Science. 1997;277:1453–1474. - PubMed
    1. Chaisson MJ, Pevzner PA. Short read fragment assembly of bacterial genomes. Genome Res. 2008;18:324–330. - PMC - PubMed
    1. Chou HH, Holmes MH. DNA sequence quality trimming and vector removal. Bioinformatics. 2001;17:1093–1104. - PubMed
    1. Denisov G, et al. Consensus generation and variant detection by Celera Assembler. Bioinformatics. 2008;24:1035–1040. - PubMed

Publication types