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      AdapterRemoval v2: rapid adapter trimming, identification, and read merging

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          Abstract

          Background

          As high-throughput sequencing platforms produce longer and longer reads, sequences generated from short inserts, such as those obtained from fossil and degraded material, are increasingly expected to contain adapter sequences. Efficient adapter trimming algorithms are also needed to process the growing amount of data generated per sequencing run.

          Findings

          We introduce AdapterRemoval v2, a major revision of AdapterRemoval v1, which introduces (i) striking improvements in throughput, through the use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support, (ii) the ability to handle datasets containing reads or read-pairs with different adapters or adapter pairs, (iii) simultaneous demultiplexing and adapter trimming, (iv) the ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets, and (v) native gzip and bzip2 support.

          Conclusions

          We show that AdapterRemoval v2 compares favorably with existing tools, while offering superior throughput to most alternatives examined here, both for single and multi-threaded operations.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s13104-016-1900-2) contains supplementary material, which is available to authorized users.

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          Most cited references19

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            Cutadapt removes adapter sequences from high-throughput sequencing reads

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              FLASH: fast length adjustment of short reads to improve genome assemblies.

              Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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                Author and article information

                Contributors
                MikkelSch@gmail.com , MSchubert@snm.ku.dk
                stinus.lindgreen@gmail.com
                Lorlando@snm.ku.dk
                Journal
                BMC Res Notes
                BMC Res Notes
                BMC Research Notes
                BioMed Central (London )
                1756-0500
                12 February 2016
                12 February 2016
                2016
                : 9
                : 88
                Affiliations
                [ ]Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark
                [ ]Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
                [ ]Carlsberg Research Laboratory, Gamle Carlsberg Vej 4-10, 1799 Copenhagen, Denmark
                [ ]Laboratoire AMIS, Université de Toulouse, University Paul Sabatier (UPS), CNRS UMR 5288, 37 Allées Jules Guesde, 31000 Toulouse, France
                Author information
                http://orcid.org/0000-0003-2401-9921
                Article
                1900
                10.1186/s13104-016-1900-2
                4751634
                26868221
                567c9119-382d-4888-99de-b52277865d8e
                © Schubert et al. 2016

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 6 October 2015
                : 2 February 2016
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100003554, Lundbeckfonden;
                Award ID: R52-A5062
                Award Recipient :
                Funded by: Marie Curie International Outgoing Fellowship
                Funded by: FundRef http://dx.doi.org/10.13039/501100004836, Det Frie Forskningsråd (DK);
                Award ID: FNU-4002-00152B
                Award Recipient :
                Funded by: Danish National Research Foundation
                Award ID: DNRF94
                Award Recipient :
                Funded by: IDEX, Université of Toulouse
                Award ID: Chaires d’Attractivité 2014
                Award Recipient :
                Categories
                Technical Note
                Custom metadata
                © The Author(s) 2016

                Medicine
                adapter identification,adapter trimming,data pre-processing,high-throughput sequencing,sequence alignment

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