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

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

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Blanca Postigo, JM.; Pascual Bañuls, L.; Ziarsolo Areitioaurtena, P.; Nuez Viñals, F.; Cañizares Sales, J. (2011). Ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence. BMC Genomics. 12:1-8. doi:10.1186/1471-2164-12-285

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/27868

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Title: Ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence
Author:
UPV Unit: Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia
Issued date:
Abstract:
Background: The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping ...[+]
Subjects: Framework , Discovery , Transcriptome , Lycoperson-Esculentum
Copyrigths: Reconocimiento (by)
Source:
BMC Genomics. (issn: 1471-2164 )
DOI: 10.1186/1471-2164-12-285
Publisher:
BioMed Central
Publisher version: http://www.biomedcentral.com/1471-2164/12/285
Type: Artículo

References

Metzker ML: Sequencing technologies - the next generation. Nature Reviews Genetics. 2010, 11 (1): 31-46. 10.1038/nrg2626.

454 sequencing. [ http://www.454.com/ ]

Illumina Inc. [ http://www.illumina.com/ ] [+]
Metzker ML: Sequencing technologies - the next generation. Nature Reviews Genetics. 2010, 11 (1): 31-46. 10.1038/nrg2626.

454 sequencing. [ http://www.454.com/ ]

Illumina Inc. [ http://www.illumina.com/ ]

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.

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.

Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25 (14): 1754-1760. 10.1093/bioinformatics/btp324.

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):

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.

1000 Genomes. A deep Catalog of Human Genetic Variation. [ http://1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf4.0 ]

The seqanswers internet forum. [ http://seqanswers.com/ ]

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.

CloVR Automated Sequence Analysis from Your Desktop. [ http://clovr.org/ ]

Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG: Next generation transcriptomes for next generation genomes using est2assembly. Bmc Bioinformatics. 2009, 10:

Applied Biosystems by life technologies. [ http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing.html ]

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:

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.

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:

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.

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.

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.

Rick CM: Tomato, Lycopersicon esculentum (Solanaceae). Evolution of crop plants. Edited by: Simmonds NW. 1976, London: Longman Group, 268-273.

Labate JA, Baldo AM: Tomato SNP discovery by EST mining and resequencing. Molecular Breeding. 2005, 16 (4): 343-349. 10.1007/s11032-005-1911-5.

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.

Jimenez-Gomez JM, Maloof JN: Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. Bmc Plant Biology. 2009, 9:

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.

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:

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:

Bioinformatics at COMAV. [ http://bioinf.comav.upv.es/ngs_backbone/index.html ]

Broad institute. [ http://www.broadinstitute.org/igv ]

Bioinformatics at COMAV. [ http://bioinf.comav.upv.es/ngs_backbone/install.html ]

Github social coding. [ http://github.com/JoseBlanca/franklin ]

Chou HH, Holmes MH: DNA sequence quality trimming and vector removal. Bioinformatics. 2001, 17 (12): 1093-1104. 10.1093/bioinformatics/17.12.1093.

Picard. [ http://picard.sourceforge.net/index.shtml ]

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.

Sol Genomics Network. [ ftp://ftp.solgenomics.net/ ]

NCBI Genbank. [ http://www.ncbi.nlm.nih.gov/genbank/ ]

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.

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