Ngs_backbone: A pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Blanca, Jose M ^a   Pascual, Laura ^a   Ziarsolo, Peio ^a   Nuez, Fernando ^a   Cañizares, Joaquin ^a  

^a UNIVERSITAT POLITÈCNICA DE VALÈNCIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ACCURACY; ARTICLE; BIOINFORMATICS; COMPUTER MODEL; COMPUTER PROGRAM; EXPRESSED SEQUENCE TAG; GENE MAPPING; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC SELECTION; MOLECULAR GENETICS; NEXT GENERATION SEQUENCE; NONHUMAN; PREDICTION; SINGLE NUCLEOTIDE POLYMORPHISM; TOMATO; ALGORITHM; BIOLOGY; DOCUMENTATION; GENETICS; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; REPRODUCIBILITY; STATISTICS;

LYCOPERSICON ESCULENTUM;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DOCUMENTATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LYCOPERSICON ESCULENTUM; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SOFTWARE; STATISTICS AS TOPIC;

EID: 79959575830     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-285     Document Type: Article

References (37)

1. Metzker ML. Sequencing technologies - the next generation. Nature Reviews Genetics 2010, 11(1):31-46. 10.1038/nrg2626, 19997069.
2. 454 sequencing. , http://www.454.com/
3. Illumina Inc. , http://www.illumina.com/
4. Flicek P, Birney E. Sense from sequence reads: methods for alignment and assembly (vol 6, pg S6, 2009). Nature Methods 2010, 7(6):479-479.
5. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Muller WEG, Wetter T, Suhai S. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Research 2004, 14(6):1147-1159. 10.1101/gr.1917404, 419793, 15140833.
6. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
7. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 2009, 10(3).
8. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, . Genome Project Data P The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943, Genome Project Data P.
9. 1000 Genomes. A deep Catalog of Human Genetic Variation. , http://1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf4.0
10. The seqanswers internet forum. , http://seqanswers.com/
11. Blankenberg D, Taylor J, Schenck I, He JB, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Ross CH, Nekrutenko A. A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly. Genome Research 2007, 17(6):960-964. 10.1101/gr.5578007, 1891355, 17568012.
12. CloVR Automated Sequence Analysis from Your Desktop. , http://clovr.org/
13. Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG. Next generation transcriptomes for next generation genomes using est2assembly. Bmc Bioinformatics 2009, 10.
14. Applied Biosystems by life technologies. , http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing.html
15. Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang HY, Landherr L, Tomsho LP, Hu Y, Carlson JE, Ma H, Schuster SC, Soltis DE, Soltis PS, Altman N, dePamphilis CW. Comparison of next generation sequencing technologies for transcriptome characterization. Bmc Genomics 2009, 10.
16. Murchison EP, Tovar C, Hsu A, Bender HS, Kheradpour P, Rebbeck CA, Obendorf D, Conlan C, Bahlo M, Blizzard CA, Pyecroft S, Kreiss A, Kellis M, Stark A, Harkins TT, Marshall Graves JA, Woods GM, Hanon GJ, Papenfuss AT. The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer. Science 2010, 327(5961):84-87. 10.1126/science.1180616, 2982769, 20044575.
17. Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. Bmc Genomics 2010, 11.
18. Babik W, Stuglik M, Qi W, Kuenzli M, Kuduk K, Koteja P, Radwan J. Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate. BMC Genomics 2010, 11:390. 10.1186/1471-2164-11-390, 2996923, 20565972.
19. Miller JC, Tanksley SD. RFLP analysis of phylogenetic-relationships and genetic-variation in the genus Lycopersicon. Theoretical and Applied Genetics 1990, 80(4):437-448.
20. Williams CE, Stclair DA. Phenetic relationships and levels of variability detected by restriction-fragment-length-polymorphism and random amplified polymorphic DNA analysis of cultivated and wild accessions of Lycopersicon-esculentum. Genome 1993, 36(3):619-630. 10.1139/g93-083, 18470012.
21. Rick CM. Tomato, Lycopersicon esculentum (Solanaceae). Evolution of crop plants 1976, 268-273. London: Longman Group, Simmonds NW.
22. Labate JA, Baldo AM. Tomato SNP discovery by EST mining and resequencing. Molecular Breeding 2005, 16(4):343-349.
23. Yano K, Watanabe M, Yamamoto N, Maeda F, Tsugane T, Shibata D. Expressed sequence tags (EST) database of a miniature tomato cultivar, Micro-Tom. Plant and Cell Physiology 2005, 46:S139-S139.
24. Jimenez-Gomez JM, Maloof JN. Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. Bmc Plant Biology 2009, 9.
25. Yang WC, Bai XD, Kabelka E, Eaton C, Kamoun S, van der Knaap E, Francis D. Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags. Molecular Breeding 2004, 14(1):21-34.
26. Van Deynze A, Stoffel K, Buell CR, Kozik A, Liu J, van der Knaap E, Francis D. Diversity in conserved genes in tomato. Bmc Genomics 2007, 8.
27. Sim SC, Robbins MD, Chilcott C, Zhu T, Francis DM. Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding. Bmc Genomics 2009, 10.
28. Bioinformatics at COMAV. , http://bioinf.comav.upv.es/ngs_backbone/index.html
29. Broad institute. , http://www.broadinstitute.org/igv
30. Bioinformatics at COMAV. , http://bioinf.comav.upv.es/ngs_backbone/install.html
31. Github social coding. , http://github.com/JoseBlanca/franklin
32. Chou HH, Holmes MH. DNA sequence quality trimming and vector removal. Bioinformatics 2001, 17(12):1093-1104. 10.1093/bioinformatics/17.12.1093, 11751217.
33. Picard. , http://picard.sourceforge.net/index.shtml
34. McKenna A, Hanna M, Banks E, Sivachenko A, Citulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 2010, 20:1297-1303. 10.1101/gr.107524.110, 2928508, 20644199.
35. Sol Genomics Network. , ftp://ftp.solgenomics.net/
36. NCBI Genbank. , http://www.ncbi.nlm.nih.gov/genbank/
37. Gundry CN, Vandersteen JG, Reed GH, Pryor RJ, Chen J, Wittwer CT. Amplicon melting analysis with labeled primers: A closed-tube method for differentiating homozygotes and heterozygotes. Clinical Chemistry 2003, 49(3):396-406. 10.1373/49.3.396, 12600951.