BESST - Efficient scaffolding of large fragmented assemblies

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Sahlin, Kristoffer ^a   Vezzi, Francesco ^a   Nystedt, Björn ^b   Lundeberg, Joakim ^a   Arvestad, Lars ^b  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^b STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

Genome analysis; Genome assembly; Mate pair next generation sequencing; Scaffolding

Indexed keywords

GENES;

COMPREHENSIVE COMPARISONS; DE NOVO ASSEMBLIES; GENOME ANALYSIS; GENOME ASSEMBLY; HIGH-THROUGHPUT SEQUENCING; INFORMATION SOURCES; NEXT-GENERATION SEQUENCING; SCAFFOLDING;

SCAFFOLDS;

ALGORITHM; ARTICLE; COMPUTER PROGRAM; DNA SEQUENCE; GENE LIBRARY; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METHODOLOGY; REPRODUCIBILITY;

ALGORITHMS; GENE LIBRARY; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84906826446     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-281     Document Type: Article

References (28)

1. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18(5):821-829.
2. MacCallum I, Przybylski D, Gnerre S, Burton J, Shlyakhter I, Gnirke A, Malek J, McKernan K, Ranade S, Shea TP, Williams L, Young S, Nusbaum C, Jaffe DB. ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol 2009, 10(10):103.
3. Richter DC, Schuster SC, Huson DH. OSLay: optimal syntenic layout of unfinished assemblies. Bioinformatics (Oxford, England) 2007, 23(13):1573-1579.
4. Nagarajan N, Read TD, Pop M. Scaffolding and validation of bacterial genome assemblies using optical scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics 2008, 24:1229-1235.
5. Mortazavi A, Schwarz E, Williams B, Schaeffer L, Antoshechkin I, Wold B, Sternberg P. Scaffolding a Caenorhabditis nematode genome with RNA-seq. Genome Res 2010, 20(12):1740-1747.
6. Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin Y-C, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Ha¨llman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Ka¨ller M, Luthman J, Lysholm F, Rilakovic N, Ritland C, Sena J, et al. Niittyla¨ T The Norway spruce genome sequence and conifer genome evolution. Nature 2013, 497(7451):579-584. Niittyla¨ T.
7. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marcais G, Pop M, Yorke JA. GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res 2012, 22(3):557-567.
8. Hunt M, Newbold C, Berriman M, Otto T. A comprehensive evaluation of assembly scaffolding tools. Genome Biol 2014, 15(3):42.
9. Huson DH, Reinert K, Myers EW. The greedy path-merging algorithm for contig scaffolding. J ACM 2002, 49(5):603-615.
10. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 2011, 27(4):578-579.
11. Pop M, Kosack DS, Salzberg SL. Hierarchical scaffolding with Bambus. Genome Res 2004, 14(1):149-159.
12. Dayarian A, Michael TP, Sengupta AM. SOPRA: scaffolding algorithm for paired reads via statistical optimization. BMC Bioinformatics 2010, 11:345.
13. Gao S, Sung W-K, Nagarajan N. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. J Comput Biol 2011, 18(11):1681-1691.
14. Roy RS, Chen KC, Sengupta AM, Schliep A. SLIQ: Simple linear inequalities for efficient contig scaffolding. J Comput Biol 2012, 19(10):1162-1175.
15. Salmela L, Ma¨kinen V, Va¨lima¨ki N, Ylinen J, Ukkonen E. Fast scaffolding with small independent mixed integer programs. Bioinformatics 2011, 27(23):3259-3265.
16. Gritsenko AA, Nijkamp JF, Reinders MJ, de Ridder D. GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies. Bioinformatics 2012, 28(11):1429-1437.
17. Sahlin K, Street N, Lundeberg J, Arvestad L. Improved gap size estimation for scaffolding algorithms. Bioinformatics 2012, 28(17):2215-2222.
18. Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol I, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res 2011, 21(12):2224-2241.
19. Vezzi F, Narzisi G, Mishra B. Feature-by-feature-evaluating de novo sequence assembly. PLoS ONE 2012, 7(2):31002.
20. Vezzi F, Narzisi G, Mishra B. Reevaluating assembly evaluations with feature response curves: GAGE and assemblathons. PLoS ONE 2012, 7(12):52210.
21. Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics 2010, 95(6):315-327.
22. Ribeiro FJ, Przybylski D, Yin S, Sharpe T, Gnerre S, Abouelleil A, Berlin AM, Montmayeur A, Shea TP, Walker BJ, Young SK, Russ C, Nusbaum C, MacCallum I, Jaffe DB. Finished bacterial genomes from shotgun sequence data. Genome Res 2012, 22(11):2270-2277.
23. Picard. [http://picard.sourceforge.net].
24. Kolmogorov AN. Sulla determinazione empirica di una legge di distribuzione (On the empirical determination of a distribution law). Giornale dell'Istituto Italiano degli Attuari 1933, 4:83-91.
25. Networkx. [http://networkx.lanl.gov/].
26. Pysam. [http://code.google.com/p/pysam/].
27. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26(5):589-595.
28. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):25.