Kraken: A set of tools for quality control and analysis Of high-throughput sequence data

被引：293

作者：

Davis, Matthew P. A. ^{[1
]}

van Dongen, Stijn ^{[1
]}

Abreu-Goodger, Cei ^{[2
]}

Bartonicek, Nenad ^{[1
]}

Enright, Anton J. ^{[1
]}

机构：

[1] EMBL European Bioinformat Inst, Cambridge CB10 1SD, England

[2] Natl Lab Genom Biodivers Langebio, Guanajuato, Mexico

来源：

METHODS | 2013年 / 63卷 / 01期

基金：

英国生物技术与生命科学研究理事会;

关键词：

Algorithms; Tools; RNAseq; NGS; Next-generation sequencing; Sequencing; Adapter trimming; Pipelines;

D O I：

10.1016/j.ymeth.2013.06.027

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

New sequencing technologies pose significant challenges in terms of data complexity and magnitude. It is essential that efficient software is developed with performance that scales with this growth in sequence information. Here we present a comprehensive and integrated set of tools for the analysis of data from large scale sequencing experiments. It supports adapter detection and removal, demultiplexing of barcodes, paired-end data, a range of read architectures and the efficient removal of sequence redundancy. Sequences can be trimmed and filtered based on length, quality and complexity. Quality control plots track sequence length, composition and summary statistics with respect to genomic annotation. Several use cases have been integrated into a single streamlined pipeline, including both mRNA and small RNA sequencing experiments. This pipeline interfaces with existing tools for genomic mapping and differential expression analysis. (C) 2013 The Authors. Published by Elsevier Inc. All rights reserved.

引用

页码：41 / 49

页数：9

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