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
Genetic variants regulating immune cell levels in health and disease
Valeria Orrù,Maristella Steri,Gabriella Sole,Carlo Sidore,Carlo Sidore,Francesca Virdis,Mariano Dei,Sandra Lai,Magdalena Zoledziewska,Fabio Busonero,Antonella Mulas,Matteo Floris,Wieslawa I. Mentzen,Silvana Anna Maria Urru,Stefania Olla,Michele Marongiu,Maria Grazia Piras,Monia Lobina,Andrea Maschio,Maristella Pitzalis,Maria Francesca Urru,Marco Marcelli,Roberto Cusano,Francesca Deidda,Valentina Serra,Manuela Oppo,Rosella Pilu,Frederic Reinier,Riccardo Berutti,Luca Pireddu,Ilenia Zara,Eleonora Porcu,Alan Kwong,Christine Brennan,Brendan Tarrier,Robert H. Lyons,Hyun Min Kang,Sergio Uzzau,Rossano Atzeni,M. Valentini,Davide Firinu,Lidia Leoni,Gianluca Rotta,Silvia Naitza,Andrea Angius,Mauro Congia,Michael B. Whalen,Chris Jones,David Schlessinger,Gonçalo R. Abecasis,Edoardo Fiorillo,Serena Sanna,Francesco Cucca +52 more
TL;DR: Genetic contributions to quantitative levels of 95 cell types encompassing 272 immune traits, in a cohort of 1,629 individuals from four clustered Sardinian villages are reported, connecting specific cellular phenotypes to specific genetic variants, helping to explicate their involvement in disease.
Journal ArticleDOI
Base-Resolution Mapping Reveals Distinct m1A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts
Xiaoyu Li,Xushen Xiong,Meiling Zhang,Kun Wang,Ying Chen,Jun Zhou,Yuanhui Mao,Jia Lv,Danyang Yi,Xiao Wei Chen,Chu Wang,Shu-Bing Qian,Chengqi Yi +12 more
TL;DR: A base-resolution m1A profiling method is developed, based onm1A-induced misincorporation during reverse transcription, and distinct classes of m1 a methylome are revealed in the human transcriptome, providing a resource for functional studies of m 1A-mediated epitranscriptomic regulation.
Journal ArticleDOI
Tools for mapping high-throughput sequencing data
TL;DR: This survey focuses on classifying mappers through a wide number of characteristics to allow practitioners to compare the mappers more easily and find those that are most suitable for their specific problem.
Journal ArticleDOI
Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis
Jamie M J Weaver,Caryn S. Ross-Innes,Nicholas B. Shannon,Andy G. Lynch,Tim Forshew,Mariagnese Barbera,Muhammed Murtaza,Chin-Ann Johnny Ong,Pierre Lao-Sirieix,Mark J Dunning,Laura Smith,Mike L. Smith,Charlotte Anderson,Benilton S. Carvalho,Maria O'Donovan,Timothy J. Underwood,Andrew May,Nicola Grehan,Richard H. Hardwick,Jim Davies,Arusha Oloumi,Samuel Aparicio,Carlos Caldas,Matthew D. Eldridge,Paul A.W. Edwards,Nitzan Rosenfeld,Simon Tavaré,Rebecca C. Fitzgerald +27 more
TL;DR: In conclusion, mutations in EAC driver genes generally occur exceptionally early in disease development with profound implications for diagnostic and therapeutic strategies.
Journal ArticleDOI
Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing
Anna Casasent,Aislyn Schalck,Ruli Gao,Emi Sei,Annalyssa N. Long,William Pangburn,Tod D. Casasent,Funda Meric-Bernstam,Mary E. Edgerton,Nicholas Navin +9 more
TL;DR: Topographic Single Cell Sequencing data reveal a direct genomic lineage between in situ and invasive tumor subpopulations and further show that most mutations and copy number aberrations evolved within the ducts prior to invasion.
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.