Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Methods. 2013 Sep 1;63(1):41-9. doi: 10.1016/j.ymeth.2013.06.027. Epub 2013 Jun 29.

Kraken: a set of tools for quality control and analysis of high-throughput sequence data.

Author information

  • 1EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

Abstract

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.

Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

KEYWORDS:

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

PMID:
23816787
[PubMed - indexed for MEDLINE]
PMCID:
PMC3991327
Free PMC Article

Images from this publication.See all images (5)Free text

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for PubMed Central
    Loading ...
    Write to the Help Desk