Kraken: A set of tools for quality control and analysis of high-throughput sequence data
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TLDR
A comprehensive and integrated set of tools for the analysis of data from large scale sequencing experiments, which supports adapter detection and removal, demultiplexing of barcodes, paired-end data, a range of read architectures and the efficient removal of sequence redundancy.About:
This article is published in Methods.The article was published on 2013-09-01 and is currently open access. It has received 361 citations till now. The article focuses on the topics: Alignment-free sequence analysis & Large-Scale Sequencing.read more
Citations
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UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
TL;DR: It is shown that errors in the UMI sequence are common and network-based methods to account for these errors when identifying PCR duplicates are introduced, demonstrating the value of properly accounting for errors in UMIs.
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AdapterRemoval v2: rapid adapter trimming, identification, and read merging.
TL;DR: It is shown that AdapterRemoval v2 compares favorably with existing tools, while offering superior throughput to most alternatives examined here, both for single and multi-threaded operations.
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Computational and analytical challenges in single-cell transcriptomics
TL;DR: The development of high-throughput RNA sequencing at the single-cell level has already led to profound new discoveries in biology, ranging from the identification of novel cell types to the study of global patterns of stochastic gene expression.
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Genetic compensation triggered by mutant mRNA degradation
Mohamed A. El-Brolosy,Zacharias Kontarakis,Andrea Rossi,Andrea Rossi,Carsten Kuenne,Stefan Günther,Nana Fukuda,Khrievono Kikhi,Giulia L. M. Boezio,Carter M. Takacs,Carter M. Takacs,Shih-Lei Lai,Shih-Lei Lai,Ryuichi Fukuda,Claudia Gerri,Claudia Gerri,Antonio J. Giraldez,Didier Y.R. Stainier +17 more
TL;DR: Transcriptional adaptation, a genetic compensation process by which organisms respond to mutations by upregulating related genes, is triggered by mRNA decay and involves a sequence-dependent mechanism.
Journal ArticleDOI
Cellular senescence drives age-dependent hepatic steatosis.
Mikolaj Ogrodnik,Satomi Miwa,Tamar Tchkonia,Dina Tiniakos,Dina Tiniakos,Caroline L. Wilson,Albert Lahat,Christopher P. Day,Christopher P. Day,Alastair D. Burt,Alastair D. Burt,Allyson K. Palmer,Quentin M. Anstee,Sushma Nagaraja Grellscheid,Jan H.J. Hoeijmakers,Jan H.J. Hoeijmakers,Sander Barnhoorn,Derek A. Mann,Thomas G. Bird,Wilbert P. Vermeij,James L. Kirkland,João F. Passos,Thomas von Zglinicki,Diana Jurk +23 more
TL;DR: It is demonstrated that cellular senescence drives hepatic Steatosis and elimination of senescent cells may be a novel therapeutic strategy to reduce steatosis.
References
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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
TL;DR: 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.
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Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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Cutadapt removes adapter sequences from high-throughput sequencing reads
TL;DR: The command-line tool cutadapt is developed, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.
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Bioconductor: open software development for computational biology and bioinformatics
Robert Gentleman,Vincent J. Carey,Douglas M. Bates,Benjamin M. Bolstad,Marcel Dettling,Sandrine Dudoit,Byron Ellis,Laurent Gautier,Yongchao Ge,Jeff Gentry,Kurt Hornik,Torsten Hothorn,Wolfgang Huber,Stefano Maria Iacus,Rafael A. Irizarry,Friedrich Leisch,Cheng Li,Martin Maechler,A. J. Rossini,Günther Sawitzki,Colin A. Smith,Gordon K. Smyth,Luke Tierney,Jean Yang,Jianhua Zhang +24 more
TL;DR: Details of the aims and methods of Bioconductor, the collaborative creation of extensible software for computational biology and bioinformatics, and current challenges are described.
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miRBase: integrating microRNA annotation and deep-sequencing data
Ana Kozomara,Sam Griffiths-Jones +1 more
TL;DR: This work has mapped reads from short RNA deep-sequencing experiments to microRNAs in miRBase and developed web interfaces to view these mappings, which can be used as a proxy for relative expression levels of microRNA sequences, provide detailed evidence for microRNA annotations and alternative isoforms of mature micro RNAs, and allow us to revisit previous annotations.