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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Exome sequencing and the genetic basis of complex traits
Adam Kiezun,Kiran V. Garimella,Ron Do,Ron Do,Nathan O. Stitziel,Nathan O. Stitziel,Benjamin M. Neale,Benjamin M. Neale,Paul J. McLaren,Paul J. McLaren,Namrata Gupta,Pamela Sklar,Patrick F. Sullivan,Jennifer L. Moran,Christina M. Hultman,Paul Lichtenstein,Patrik K. E. Magnusson,Thomas Lehner,Yin Yao Shugart,Alkes L. Price,Alkes L. Price,Paul I.W. de Bakker,Paul I.W. de Bakker,Paul I.W. de Bakker,Shaun Purcell,Shamil R. Sunyaev,Shamil R. Sunyaev +26 more
TL;DR: Exome sequencing methods and their applications in studies to identify the genetic basis of human complex traits are presented and include analyses of the whole-exome sequences of 438 individuals from across several studies.
Journal ArticleDOI
Promiscuous RNA binding by Polycomb repressive complex 2
Chen Davidovich,Leon Zheng,Karen J. Goodrich,Karen J. Goodrich,Thomas R. Cech,Thomas R. Cech +5 more
TL;DR: These findings support a model in which PRC2's promiscuous binding to RNA transcripts allows it to scan for target genes that have escaped repression, thus leading to maintenance of the repressed state.
Journal ArticleDOI
Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars
Mingzhou Li,Shilin Tian,Long Jin,Guangyu Zhou,Ying Li,Yuan Zhang,Tao Wang,Carol K.L. Yeung,Lei Chen,Jideng Ma,Jinbo Zhang,Anan Jiang,Ji Li,Chaowei Zhou,Jie Zhang,Yingkai Liu,Xiaoqing Sun,Hongwei Zhao,Zexiong Niu,Pinger Lou,Lingjin Xian,Xiaoyong Shen,Shaoqing Liu,Shunhua Zhang,Mingwang Zhang,Li Zhu,Surong Shuai,Lin Bai,Guoqing Tang,Haifeng Liu,Yanzhi Jiang,Miaomiao Mai,Jian Xiao,Xun Wang,Qi Zhou,Zhiquan Wang,Paul Stothard,Ming Xue,Xiaolian Gao,Zonggang Luo,Yiren Gu,Hongmei Zhu,Xiaoxiang Hu,Yaofeng Zhao,Graham Plastow,Jinyong Wang,Zhi Jiang,Kui Li,Ning Li,Xuewei Li,Ruiqiang Li +50 more
TL;DR: Comparing the genome of Tibetan wild boars with those of neighboring Chinese domestic pigs further showed the impact of thousands of years of artificial selection and different signatures of selection in wild boar and domestic pig.
Journal ArticleDOI
Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA
TL;DR: Examination of mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular features finds that fragment length does not decrease consistently over time and that strand breaks occur preferentially before purine residues by what may be at least two different molecular mechanisms that are not yet understood.
Journal ArticleDOI
Molecular profiling of the residual disease of triple-negative breast cancers after neoadjuvant chemotherapy identifies actionable therapeutic targets
Justin M. Balko,Jennifer M. Giltnane,Kai Wang,Luis J. Schwarz,Christian D. Young,Rebecca S. Cook,Philip Owens,Melinda E. Sanders,Maria G. Kuba,Violeta Sanchez,Richard Kurupi,Preston D. Moore,Joseph A. Pinto,Franco Doimi,Henry L. Gomez,Dai Horiuchi,Andrei Goga,Brian D. Lehmann,Joshua A. Bauer,Jennifer A. Pietenpol,Jeffrey S. Ross,Gary A. Palmer,Roman Yelensky,Maureen T. Cronin,Vincent A. Miller,Phillip J. Stephens,Carlos L. Arteaga +26 more
TL;DR: In this article, the authors performed molecular analyses on the residual disease (RD) of 74 clinically-defined triple-negative breast cancers after NAC including next-generation sequencing (NGS) on 20 matched pre-treatment biopsies and combined NGS and digital RNA expression analysis identified diverse molecular lesions and pathway activation in drugresistant tumor cells.
References
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