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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Journal ArticleDOI
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
Joshua Quick,Nathan D. Grubaugh,Steven T. Pullan,Ingra Morales Claro,Andrew D. Smith,Karthik Gangavarapu,Glenn Oliveira,Refugio Robles-Sikisaka,Thomas F. Rogers,Thomas F. Rogers,Nathan Beutler,Dennis R. Burton,Lia Laura Lewis-Ximenez,Jaqueline Goes de Jesus,Marta Giovanetti,Marta Giovanetti,Sarah C. Hill,Allison Black,Allison Black,Trevor Bedford,Miles W. Carroll,Márcio Roberto Teixeira Nunes,Luiz Carlos Junior Alcantara,Ester Cerdeira Sabino,Sally A. Baylis,Nuno R. Faria,Matthew Loose,Jared T. Simpson,Oliver G. Pybus,Kristian G. Andersen,Kristian G. Andersen,Nicholas J. Loman +31 more
TL;DR: A protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences.
Journal ArticleDOI
A new genomic blueprint of the human gut microbiota
Alexandre Almeida,Alex L. Mitchell,Miguel Boland,Samuel C. Forster,Gregory B. Gloor,Aleksandra Tarkowska,Trevor D. Lawley,Robert D. Finn +7 more
TL;DR: The known species repertoire of the collective human gut microbiota is substantially expanded with the discovery of 1,952 uncultured bacterial species that greatly improve classification of understudied African and South American samples.
Journal ArticleDOI
Expression of Linear and Novel Circular Forms of an INK4/ARF-Associated Non-Coding RNA Correlates with Atherosclerosis Risk
TL;DR: The results identify novel circular RNA products emanating from the ANRIL locus and suggest causal variants at 9p21.3 regulate INK4/ARF expression and ASVD risk by modulating ANRil expression and/or structure.
Journal ArticleDOI
Comparative population genomics of maize domestication and improvement
Matthew B. Hufford,Xun Xu,Joost van Heerwaarden,Tanja Pyhäjärvi,Jer Ming Chia,Reed A. Cartwright,Robert J. Elshire,Jeffrey C. Glaubitz,Kate E. Guill,Kate E. Guill,Shawn M. Kaeppler,Jinsheng Lai,Peter L. Morrell,Laura M. Shannon,Chi Song,Nathan M. Springer,Ruth A. Swanson-Wagner,Peter Tiffin,Jun Wang,Gengyun Zhang,John Doebley,Michael D. McMullen,Michael D. McMullen,Doreen Ware,Doreen Ware,Edward S. Buckler,Edward S. Buckler,Shuang Yang,Jeffrey Ross-Ibarra +28 more
TL;DR: A comprehensive assessment of the evolution of modern maize based on the genome-wide resequencing of 75 wild, landrace and improved maize lines finds evidence of recovery of diversity after domestication, likely introgression from wild relatives, and evidence for stronger selection during domestication than improvement.
Journal ArticleDOI
Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators
Akihiro Fujimoto,Yasushi Totoki,Tetsuo Abe,Keith A. Boroevich,Fumie Hosoda,Ha Hai Nguyen,Masayuki Aoki,Naoya Hosono,Michiaki Kubo,Fuyuki Miya,Yasuhito Arai,Hiroyuki Takahashi,Takuya Shirakihara,Masao Nagasaki,Tetsuo Shibuya,Kaoru Nakano,Kumiko Watanabe-Makino,Hiroko Tanaka,Hiromi Nakamura,Jun Kusuda,Hidenori Ojima,Kazuaki Shimada,Takuji Okusaka,Masaki Ueno,Yoshinobu Shigekawa,Yoshiiku Kawakami,Koji Arihiro,Hideki Ohdan,Kunihito Gotoh,Osamu Ishikawa,Shunichi Ariizumi,Masakazu Yamamoto,Terumasa Yamada,Kazuaki Chayama,Tomoo Kosuge,Hiroki Yamaue,Naoyuki Kamatani,Satoru Miyano,Hitoshi Nakagama,Yusuke Nakamura,Tatsuhiko Tsunoda,Tatsuhiro Shibata,Hidewaki Nakagawa +42 more
TL;DR: The whole-genome sequencing analysis of HCCs identified the influence of etiological background on somatic mutation patterns and subsequent carcinogenesis, as well as recurrent mutations in chromatin regulators in H CCs.
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