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      GenomeScope: fast reference-free genome profiling from short reads

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          Abstract

          GenomeScope is an open-source web tool to rapidly estimate the overall characteristics of a genome, including genome size, heterozygosity rate and repeat content from unprocessed short reads. These features are essential for studying genome evolution, and help to choose parameters for downstream analysis. We demonstrate its accuracy on 324 simulated and 16 real datasets with a wide range in genome sizes, heterozygosity levels and error rates.

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          Informed and automated k-mer size selection for genome assembly.

          Rayan Chikhi, Paul Medvedev (2014)
          Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically estimate the best k to use and/or quickly generate histograms of k-mer abundances that would allow the user to make an informed decision. We develop a fast and accurate sampling method that constructs approximate abundance histograms with several orders of magnitude performance improvement over traditional methods. We then present a fast heuristic that uses the generated abundance histograms for putative k values to estimate the best possible value of k. We test the effectiveness of our tool using diverse sequencing datasets and find that its choice of k leads to some of the best assemblies. Our tool KmerGenie is freely available at: http://kmergenie.bx.psu.edu/.
          Article 0 comments Cited 341 times – based on 0 reviews     Review now
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            Nonlinear Regression Analysis and Its Applications

            Douglas Bates, Donald G. Watts (1988)
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              Quake: quality-aware detection and correction of sequencing errors

              David R. Kelley, Michael Schatz, Steven Salzberg (2010)
              We introduce Quake, a program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates, Quake achieves the highest accuracy on realistically simulated reads. We further demonstrate substantial improvements in de novo assembly and SNP detection after using Quake. Quake can be used for any size project, including more than one billion human reads, and is freely available as open source software from http://www.cbcb.umd.edu/software/quake.
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                Author and article information

                Journal
                Title: Bioinformatics
                Publisher: Oxford University Press (OUP)
                ISSN (Print): 1367-4803
                ISSN (Electronic): 1460-2059
                Publication date Created: July 15 2017
                Publication date Created: July 15 2017
                Publication date Created: March 24 2017
                Publication date Other: July 15 2017
                Publication date (Print): July 15 2017
                Publication date (Electronic): March 24 2017
                Volume: 33
                Issue: 14
                Pages: 2202-2204
                Affiliations
                [1 ]Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
                [2 ]Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
                [3 ]Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
                Article
                DOI: 10.1093/bioinformatics/btx153
                PubMed ID: 28369201
                SO-VID: 744757db-b83a-48cf-8174-0c4887e44ed1
                Copyright © © 2017
                License:

                https://academic.oup.com/journals/pages/about_us/legal/notices

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