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
Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences
G. David Poznik,Yali Xue,Fernando L. Mendez,Thomas Willems,Andrea Massaia,Melissa A. Wilson Sayres,Qasim Ayub,Shane A. McCarthy,Apurva Narechania,Seva Kashin,Yuan Chen,Ruby Banerjee,Juan L. Rodriguez-Flores,Maria Cerezo,Haojing Shao,Melissa Gymrek,Ankit Malhotra,Sandra Louzada,Rob DeSalle,Graham R. S. Ritchie,Graham R. S. Ritchie,Eliza Cerveira,Tomas W Fitzgerald,Erik Garrison,Anthony Marcketta,David Mittelman,Mallory Romanovitch,Chengsheng Zhang,Xiangqun Zheng-Bradley,Gonçalo R. Abecasis,Steven A. McCarroll,Paul Flicek,Peter A. Underhill,Lachlan J. M. Coin,Daniel R. Zerbino,Fengtang Yang,Charles Lee,Laura Clarke,Adam Auton,Yaniv Erlich,Robert E. Handsaker,Robert E. Handsaker,Carlos Bustamante,Chris Tyler-Smith +43 more
TL;DR: A calibrated phylogenetic tree is constructed on the basis of binary single-nucleotide variants and the more complex variants onto it, estimating the number of mutations for each class and shows bursts of extreme expansion in male numbers that have occurred independently among the five continental superpopulations examined.
Journal ArticleDOI
Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads
TL;DR: A new statistical method, MMSEQ, deconvolves the mapping of reads to multiple transcripts (isoforms or haplotype-specific isoforms) and can take into account non-uniform read generation and works with paired-end reads.
Journal ArticleDOI
ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity
Matthew D. Young,Tracy A. Willson,Matthew Wakefield,Evelyn Trounson,Douglas J. Hilton,Marnie E. Blewitt,Alicia Oshlack,Ian J. Majewski +7 more
TL;DR: This work has used ChIP-seq to generate genome-wide maps of H3K27me3 enrichment, and has identified three enrichment profiles with distinct regulatory consequences, including an enrichment profile with a peak in the promoter of genes that is associated with active transcription.
Journal ArticleDOI
Epigenetic regulation of brain region-specific microglia clearance activity
Pinar Ayata,Ana Badimon,Hayley J. Strasburger,Mary Kaye Duff,Sarah E. Montgomery,Yong-Hwee E. Loh,Anja Ebert,Anna A. Pimenova,Brianna R. Ramirez,Andrew T. Chan,Josefa M. Sullivan,Immanuel Purushothaman,Joseph R. Scarpa,Alison Goate,Meinrad Busslinger,Li Shen,Bojan Losic,Anne Schaefer +17 more
TL;DR: It is shown that microglia clearance activity in the adult brain is regionally regulated and depends on the rate of neuronal attrition, which highlights a key role of epigenetic mechanisms in preventing microglian-induced neuronal alterations that are frequently associated with neurodegenerative and psychiatric diseases.
Journal ArticleDOI
Inferring expressed genes by whole-genome sequencing of plasma DNA
Peter Ulz,Gerhard G. Thallinger,Martina Auer,Ricarda Graf,Karl Kashofer,Stephan W Jahn,Luca Abete,Gunda Pristauz,Edgar Petru,Jochen B. Geigl,Ellen Heitzer,Michael R. Speicher +11 more
TL;DR: It is found that the plasma DNA read depth patterns from healthy donors reflected the expression signature of hematopoietic cells, and in patients with cancer having metastatic disease, expressed cancer driver genes in regions with somatic copy number gains with high accuracy were classified.
References
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