NeatFreq: Reference-free data reduction and coverage normalization for sequence assembly

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  McCorrison, Jamison M ^a   Venepally, Pratap ^a   Singh, Indresh ^a   Fouts, Derrick E ^a   Lasken, Roger S ^a   Methé, Barbara A ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

Bioinformatics; Coverage reduction; de novo assembly; Multiple displacement amplification; Normalization; Single cell; SISPA; Transcriptomics

Indexed keywords

ALGORITHMS; BIOINFORMATICS; CELLS; CYTOLOGY; GENES; LABORATORIES; OPEN SOURCE SOFTWARE; OPEN SYSTEMS;

DE NOVO ASSEMBLIES; MULTIPLE DISPLACEMENT AMPLIFICATIONS; NORMALIZATION; SINGLE CELLS; SISPA; TRANSCRIPTOMICS;

DATA REDUCTION;

BACTERIA (MICROORGANISMS);

ALGORITHM; COMPUTER PROGRAM; DNA SEQUENCE; GENOMICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES;

ALGORITHMS; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84923871161     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-014-0357-3     Document Type: Article

References (30)

1. Lasken RS: Genomic sequencing of uncultured microorganisms from single cells. Nat Rev Microbiol 2012, 10:631-640.
2. Lasken RS: Genomic DNA amplification by the multiple displacement amplification (MDA) method. Biochem Soc Trans 2009, 37:450-453.
3. Raghunathan A, Ferguson HR Jr, Bornarth CJ, Song W, Driscoll M, Lasken RS: Genomic DNA amplification from a single bacterium. Appl Environ Microbiol 2005, 71:3342-3347.
4. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM: Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 2006, 24:680-686.
5. Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS: Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol 2011, 29:915-921.
6. Dupont CL, Rusch DB, Yooseph S, Lombardo MJ, Richter RA, Valas R, Novotny M, Yee-Greenbaum J, Selengut JD, Haft DH, Halpern AL, Lasken RS, Nealson K, Friedman R, Venter JC: Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J 2012, 6:1186-1199.
7. Dean FB, Nelson JR, Giesler TL, Lasken RS: Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 2001, 11:1095-1099.
8. Allen LZ, Ishoey T, Novotny MA, McLean JS, Lasken RS, Williamson SJ: Single virus genomics: a new tool for virus discovery. PLoS One 2011, 6:e17722.
9. Depew J, Zhou B, McCorrison JM, Wentworth DE, Purushe J, Koroleva G, Fouts DE: Sequencing viral genomes from a single isolated plaque. Virol J 2013, 10:181.
10. Yokouchi H, Fukuoka Y, Mukoyama D, Calugay R, Takeyama H, Matsunaga T: Whole-metagenome amplification of a microbial community associated with scleractinian coral by multiple displacement amplification using phi29 polymerase. Environ Microbiol 2006, 8:1155-1163.
11. Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F: Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One 2009, 4:e7370.
12. McLean JS, Lombardo MJ, Ziegler MG, Novotny M, Yee-Greenbaum J, Badger JH, Tesler G, Nurk S, Lesin V, Brami D, Hall AP, Edlund A, Allen LZ, Durkin S, Reed S, Torriana F, Nealson KH, Pevzner PA, Friedman R, Venter JC, Lasken RS: Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. Genome Res 2013, 23:867-877.
13. McLean JS, Lombardo MJ, Badger JH, Edlund A, Novotny M, Yee-Greenbaum J, Vyahhi N, Hall AP, Yang Y, Dupont CL, Ziegler MG, Chitsaz H, Allen AE, Yooseph S, Tesler G, Pevzner PA, Friedman RM, Nealson KH, Venter JC, Lasken RS: Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proc Natl Acad Sci U S A 2013, 110:E2390-E2399.
14. Brown CT, Howe A, Zhang Q, Pyrkosz AB, Brom TH: A reference-free algorithm for computational normalization of shotgun sequencing data. arXiv 2012, 1203:4802.
15. Howe AC, Jansson JK, Malfatti SA, Tringe SG, Tideje JM, Brown CT: Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci U S A 2014, 111(13):4904-4909.
16. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB: ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 2008, 18:810-820.
17. Martin M: Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 2011, 17:10-12.
18. Morgulis A, Gertz EM, Schaffer AA, Agarwala R: A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J Comput Biol 2006, 13:1028-1040.
19. Kelley DR, Schatz MC, Salzberg SL: Quake: quality-aware detection and correction of sequencing errors. Genome Biol 2010, 11:R116.
20. Bio-playground package. In https://github.com/martijnvermaat/bio-playground .
21. Quinn NL, Levenkova N, Chow W, Bouffard P, Boroevich KA, Knight JR, Jarvie TP, Lubieniecki KP, Desany BA, Koop BF, Harkins TT, Davidson WS: Assessing the feasibility of GS FLX pyrosequencing for sequencing the Atlantic salmon genome. BMC Genomics 2008, 9:404.
22. Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
23. White paper on CLC de novo assembler. In http://www.clcbio.com/files/whitepapers/whitepaper-denovo-assembly-4.pdf .
24. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, et al: The sequence of the human genome. Science 2001, 291:1304-1351.
25. Chevreux B: MIRA: An Automated Genome and EST Assembler, PhD Thesis. German Cancer Research Center Heidelberg. Department of Molecular Biophysics; 2005.
26. Kurtz S, Narechania A, Stein JC, Ware D: A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics 2008, 9:517.
27. Peng Y, Leung HC, Yiu SM, Chin FY: IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 2012, 28:1420-1428.
28. Chaisson MJ, Pevzner PA: Short read fragment assembly of bacterial genomes. Genome Res 2008, 18:324-330.
29. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012, 19:455-477.
30. Volfovsky N, Haas BJ, Salzberg SL: A clustering method for repeat analysis in DNA sequences. Genome Biol 2001, 2:RESEARCH0027.