The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
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TLDR
SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.Abstract:
Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Availability: http://samtools.sourceforge.net
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Citations
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Subsistence strategies in traditional societies distinguish gut microbiomes
Alexandra J. Obregon-Tito,Raul Y. Tito,Jessica L. Metcalf,Krithivasan Sankaranarayanan,Jose C. Clemente,Luke K. Ursell,Zhenjiang Zech Xu,Will Van Treuren,Rob Knight,Patrick M. Gaffney,Paul Spicer,Paul A. Lawson,Luis Marin-Reyes,Omar Trujillo-Villarroel,Morris W. Foster,Emilio Guija-Poma,Luzmila Troncoso-Corzo,Christina Warinner,Andrew T. Ozga,Cecil M. Lewis +19 more
TL;DR: In addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples and Treponema are discovered, which are symbionts lost in urban-industrialized societies.
Journal ArticleDOI
Passive and active DNA methylation and the interplay with genetic variation in gene regulation
Maria Gutierrez-Arcelus,Maria Gutierrez-Arcelus,Tuuli Lappalainen,Tuuli Lappalainen,Stephen B. Montgomery,Stephen B. Montgomery,Alfonso Buil,Alfonso Buil,Halit Ongen,Halit Ongen,Alisa Yurovsky,Alisa Yurovsky,Julien Bryois,Julien Bryois,Thomas Giger,Luciana Romano,Luciana Romano,Alexandra Planchon,Alexandra Planchon,Emilie Falconnet,Deborah Bielser,Maryline Gagnebin,Ismael Padioleau,Ismael Padioleau,Christelle Borel,Audrey Letourneau,Periklis Makrythanasis,Michel Guipponi,Corinne Gehrig,Stylianos E. Antonarakis,Emmanouil T. Dermitzakis,Emmanouil T. Dermitzakis +31 more
TL;DR: It is shown that unlike genetic regulatory variation, DNA methylation alone does not significantly drive allele specific expression, and inferred mechanistic relationships using genetic variation as well as correlations with TF abundance reveal both a passive and active role of DNAmethylation to regulatory interactions influencing gene expression.
Journal ArticleDOI
Spatial genomic heterogeneity within localized, multifocal prostate cancer
Paul C. Boutros,Paul C. Boutros,Michael Fraser,Nicholas J. Harding,Richard de Borja,Dominique Trudel,Emilie Lalonde,Emilie Lalonde,Alice Meng,Pablo H. Hennings-Yeomans,Andrew McPherson,Veronica Y. Sabelnykova,Amin Zia,Natalie S. Fox,Natalie S. Fox,Julie Livingstone,Yu Jia Shiah,Jianxin Wang,Timothy Beck,Cherry Have,Taryne Chong,Michelle Sam,Jeremy Johns,Lee Timms,Nicholas Buchner,Ada Wong,John D. Watson,Trent T. Simmons,Christine P'ng,Gaetano Zafarana,Francis Nguyen,Xuemei Luo,Kenneth C. Chu,Stephenie D. Prokopec,Jenna Sykes,Alan Dal Pra,Alejandro Berlin,Andrew M.K. Brown,Michelle Chan-Seng-Yue,Fouad Yousif,Robert E. Denroche,Lauren C. Chong,Gregory M. Chen,Esther Jung,Clement Fung,Maud H.W. Starmans,Hanbo Chen,Shaylan K. Govind,James R. Hawley,Alister D'Costa,Melania Pintilie,Daryl Waggott,Faraz Hach,Philippe Lambin,Lakshmi Muthuswamy,Colin Cooper,Rosalind A. Eeles,David E. Neal,David E. Neal,Bernard Têtu,Cenk Sahinalp,Lincoln Stein,Neil E. Fleshner,Sohrab P. Shah,Colin Collins,Colin Collins,Thomas J. Hudson,John Douglas Mcpherson,Theodorus van der Kwast,Robert G. Bristow +69 more
TL;DR: A new recurrent amplification of MYCL is identified and validated, which is associated with TP53 deletion and unique profiles of DNA damage and transcriptional dysregulation, and this data represents the first systematic relation of intraprostatic genomic heterogeneity to predicted clinical outcome.
Journal ArticleDOI
Sequence kernel association tests for the combined effect of rare and common variants.
TL;DR: Several sequence kernel association tests are introduced to evaluate the cumulative effect of rare and common variants and can achieve substantial increases in power compared with the most commonly used tests, including the burden and variance-component tests.
Journal ArticleDOI
Targeted Next-generation Sequencing of Advanced Prostate Cancer Identifies Potential Therapeutic Targets and Disease Heterogeneity
Himisha Beltran,Roman Yelensky,Garrett M. Frampton,Kyung Park,Sean R. Downing,Theresa Y. MacDonald,Mirna Jarosz,Doron Lipson,Scott T. Tagawa,David M. Nanus,Philip J. Stephens,Juan Miguel Mosquera,Maureen T. Cronin,Mark A. Rubin +13 more
TL;DR: This first-in-principle study demonstrates the feasibility of performing in-depth DNA analyses using FFPE tissue and brings new insight toward understanding the genomic landscape within advanced PCa.
References
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Journal ArticleDOI
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
Journal ArticleDOI
The Human Genome Browser at UCSC
W. James Kent,Charles W. Sugnet,Terrence S. Furey,Krishna M. Roskin,Tom H. Pringle,Alan M. Zahler,and David Haussler +6 more
TL;DR: A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu.
Journal ArticleDOI
Mapping short DNA sequencing reads and calling variants using mapping quality scores
Heng Li,Jue Ruan,Richard Durbin +2 more
TL;DR: This work describes the software MAQ, software that can build assemblies by mapping shotgun short reads to a reference genome, using quality scores to derive genotype calls of the consensus sequence of a diploid genome, e.g., from a human sample.
Journal ArticleDOI
Next-Generation DNA Sequencing Methods
TL;DR: An astounding potential exists for next-generation DNA sequencing technologies to bring enormous change in genetic and biological research and to enhance the authors' fundamental biological knowledge.