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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Epigenetic Priming of Memory Updating during Reconsolidation to Attenuate Remote Fear Memories
Johannes Gräff,Nadine F. Joseph,Nadine F. Joseph,Meryl E. Horn,Alireza Samiei,Jia Meng,Jia Meng,Jinsoo Seo,Jinsoo Seo,Damien Rei,Damien Rei,Adam W. Bero,Adam W. Bero,Trongha X. Phan,Trongha X. Phan,Florence F. Wagner,Edward Holson,Jinbin Xu,Jianjun Sun,Rachael L. Neve,Robert H. Mach,Stephen J. Haggarty,Li-Huei Tsai,Li-Huei Tsai +23 more
TL;DR: It is shown that, in mice, successful reconsolidation-updating paradigms for recent memories fail to attenuate remote memories, but by using an HDAC2-targeting inhibitor (HDACi) during reconsideration, even remote memories can be persistently attenuated.
Journal ArticleDOI
Exome Sequencing Identifies SMAD3 Mutations as a Cause of Familial Thoracic Aortic Aneurysm and Dissection with Intracranial and Other Arterial Aneurysms
Ellen S. Regalado,Dongchuan Guo,Carlos Villamizar,Nili Avidan,Dawna Gilchrist,Barbara McGillivray,Lorne A. Clarke,Francois P. Bernier,Regie Lyn P. Santos-Cortez,Suzanne M. Leal,Aida M. Bertoli-Avella,Jay Shendure,Mark J. Rieder,Deborah A. Nickerson,Dianna M. Milewicz +14 more
TL;DR: To identify the causative mutation in a large family with autosomal dominant inheritance of TAAD with intracranial and abdominal aortic aneurysms by performing exome sequencing of 2 distantly related individuals with TAAD and identifying shared rare variants, SMAD3 mutations are responsible for 2% of familial TAAD.
Journal ArticleDOI
Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers
Akash Kumar,Thomas A. White,Alexandra P. MacKenzie,Nigel Clegg,Choli Lee,Ruth Dumpit,Ilsa Coleman,Sarah B. Ng,Stephen J. Salipante,Mark J. Rieder,Deborah A. Nickerson,Eva Corey,Paul H. Lange,Colm Morrissey,Robert L. Vessella,Peter S. Nelson,Jay Shendure +16 more
TL;DR: The results indicate that point mutations arising in coding regions of advanced prostate cancers are common but, with notable exceptions, very few genes are mutated in a substantial fraction of tumors, and suggest that increasingly deep catalogs of human germline variation may challenge the necessity of sequencing matched tumor-normal pairs.
Journal ArticleDOI
The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology.
Eugene J. Gardner,Vincent K. Lam,Daniel N. Harris,Nelson T. Chuang,Emma C. Scott,Pittard Ws,Ryan E. Mills,Scott E. Devine +7 more
TL;DR: This study provides the most comprehensive map of MEIs to date spanning chimpanzees, ancient hominids, and modern humans and reveals new aspects of MEI biology in these lineages and is a robust platform for MEI discovery and analysis in a variety of experimental settings.
Journal ArticleDOI
Linking pangenomes and metagenomes: the Prochlorococcus metapangenome.
TL;DR: This work presents an integrated analysis and visualization strategy that provides an interactive and reproducible framework to generate pangenomes and to study them in conjunction with metagenomes and reveals potential benefits to Prochlorococcus from a high sequence diversity of sugar metabolism genes.
References
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