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
Reads0
Chats0
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
Contact: [email protected]read more
Citations
More filters
Journal ArticleDOI
Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel
Jie Huang,Bryan Howie,Shane A. McCarthy,Yasin Memari,Klaudia Walter,Josine L. Min,Petr Danecek,Giovanni Malerba,Elisabetta Trabetti,Hou-Feng Zheng,Hou-Feng Zheng,Giovanni Gambaro,J. Brent Richards,Richard Durbin,Nicholas J. Timpson,Jonathan Marchini,Jonathan Marchini,Nicole Soranzo,Nicole Soranzo +18 more
TL;DR: It is shown that large increases in imputation accuracy can be achieved by re-phasing WGS reference panels after initial genotype calling, and a method for combining WGS panels to improve variant coverage and downstream imputations accuracy is presented.
Journal ArticleDOI
Fern genomes elucidate land plant evolution and cyanobacterial symbioses
Fay-Wei Li,Fay-Wei Li,Paul Brouwer,Lorenzo Carretero-Paulet,Shifeng Cheng,Jan de Vries,Pierre-Marc Delaux,Ariana N. Eily,Nils Koppers,Li-Yaung Kuo,Zheng Li,Mathew Simenc,Ian Small,Eric K. Wafula,Stephany Angarita,Michael S. Barker,Andrea Bräutigam,Claude W. dePamphilis,Sven B. Gould,Prashant S. Hosmani,Yao Moan Huang,Bruno Huettel,Yoichiro Kato,Xin Liu,Steven Maere,Rose McDowell,Lukas A. Mueller,Klaas G.J. Nierop,Stefan A. Rensing,Tanner A. Robison,Carl J. Rothfels,Erin M. Sigel,Yue Song,Prakash R. Timilsena,Yves Van de Peer,Yves Van de Peer,Hongli Wang,Per K.I. Wilhelmsson,Paul G. Wolf,Xun Xu,Joshua P. Der,Henriette Schluepmann,Gane Ka-Shu Wong,Kathleen M. Pryer +43 more
TL;DR: The genomes of two fern species, Azolla filiculoides and Salvinia cucullata, are reported and insights into fern-specific whole-genome duplications, f Fern-specific insect-resistant gene evolution and fern–cyanobacterial symbiosis are provided.
Journal ArticleDOI
POT1 loss-of-function variants predispose to familial melanoma
Carla Daniela Robles-Espinoza,Mark Harland,Andrew J. Ramsay,Lauren G. Aoude,Víctor Quesada,Zhihao Ding,Karen A. Pooley,Antonia L. Pritchard,Jessamy Tiffen,Mia Petljak,Jane M. Palmer,Judith Symmons,Peter Johansson,Mitchell S. Stark,Michael Gartside,Helen Snowden,Grant W. Montgomery,Nicholas G. Martin,Jimmy Z. Liu,Jiyeon Choi,Matthew M. Makowski,Kevin M. Brown,Alison M. Dunning,Thomas M. Keane,Carlos López-Otín,Nelleke A. Gruis,Nicholas K. Hayward,D. Timothy Bishop,Julia Newton-Bishop,David J. Adams +29 more
TL;DR: It is shown that POT1 variants predispose to melanoma formation via a direct effect on telomeres, disrupting protein-telomere binding and leading to increased telomere length.
Journal ArticleDOI
Advances and limits of using population genetics to understand local adaptation.
Peter Tiffin,Jeffrey Ross-Ibarra +1 more
TL;DR: Important limitations to population genetic analyses are highlighted including challenges with obtaining high-quality data, deciding which loci are targets of selection, and limits to identifying the genetic basis of local adaptation.
Journal ArticleDOI
Imaging of Plasmodium Liver Stages to Drive Next-Generation Antimalarial Drug Discovery
Stephan Meister,David Plouffe,Kelli Kuhen,Ghislain M. C. Bonamy,Tao Wu,S. Whitney Barnes,Selina Bopp,Rachel Borboa,A. Taylor Bright,A. Taylor Bright,Jianwei Che,Steve Cohen,Neekesh V. Dharia,Kerstin Gagaring,Montip Gettayacamin,Perry Gordon,Todd Groessl,Nobutaka Kato,Marcus C. S. Lee,Case W. McNamara,David A. Fidock,Advait Nagle,Tae-gyu Nam,Wendy Richmond,Jason Roland,Matthias Rottmann,Matthias Rottmann,Bin Zhou,Patrick Froissard,Patrick Froissard,Richard Glynne,Dominique Mazier,Dominique Mazier,Jetsumon Sattabongkot,Peter G. Schultz,Tove Tuntland,John R. Walker,Yingyao Zhou,Arnab K. Chatterjee,Thierry T. Diagana,Elizabeth A. Winzeler,Elizabeth A. Winzeler +41 more
TL;DR: An imidazolopiperazine scaffold series was identified that was highly enriched among compounds active against Plasmodium liver stages and shows potent in vivo blood-stage therapeutic activity.
References
More filters
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.