{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T08:59:01Z","timestamp":1783414741434,"version":"3.54.6"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1937,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The continuing improvements to high-throughput sequencing (HTS) platforms have begun to unfold a myriad of new applications. As a result, error correction of sequencing reads remains an important problem. Though several tools do an excellent job of correcting datasets where the reads are sampled close to uniformly, the problem of correcting reads coming from drastically non-uniform datasets, such as those from single-cell sequencing, remains open.<\/jats:p>\n               <jats:p>Results: In this article, we develop the method Hammer for error correction without any uniformity assumptions. Hammer is based on a combination of a Hamming graph and a simple probabilistic model for sequencing errors. It is a simple and adaptable algorithm that improves on other tools on non-uniform single-cell data, while achieving comparable results on normal multi-cell data.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.cs.toronto.edu\/~pashadag.<\/jats:p>\n               <jats:p>Contact: \u00a0pmedvedev@cs.ucsd.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr208","type":"journal-article","created":{"date-parts":[[2011,6,17]],"date-time":"2011-06-17T23:32:32Z","timestamp":1308353552000},"page":"i137-i141","source":"Crossref","is-referenced-by-count":92,"title":["Error correction of high-throughput sequencing datasets with non-uniform coverage"],"prefix":"10.1093","volume":"27","author":[{"given":"Paul","family":"Medvedev","sequence":"first","affiliation":[{"name":"1 Department of Computer Science and Engineering and 2Bioinformatics Program, University of California, San Diego, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Scott","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering and 2Bioinformatics Program, University of California, San Diego, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Boyko","family":"Kakaradov","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering and 2Bioinformatics Program, University of California, San Diego, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pavel","family":"Pevzner","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering and 2Bioinformatics Program, University of California, San Diego, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,6,14]]},"reference":[{"key":"2023012512021304400_B1","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1101\/gr.7088808","article-title":"Short read fragment assembly of bacterial genomes","volume":"18","author":"Chaisson","year":"2008","journal-title":"Genome Res."},{"key":"2023012512021304400_B2","first-page":"505","volume-title":"Introduction to Algorithms","author":"Cormen","year":"2001","edition":"2nd"},{"key":"2023012512021304400_B3","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1093\/jhered\/esp086","article-title":"Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species","volume":"100","author":"Genome 10K Community of Scientists","year":"2009","journal-title":"J. Heredity"},{"key":"2023012512021304400_B4","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1126\/science.1124234","article-title":"Metagenomic analysis of the human distal gut microbiome","volume":"312","author":"Gill","year":"2006","journal-title":"Science"},{"key":"2023012512021304400_B5","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1093\/bioinformatics\/btq653","article-title":"HiTEC: accurate error correction in high-throughput sequencing data","volume":"27","author":"Ilie","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512021304400_B6","first-page":"329","volume-title":"An Introduction to Bioinformatics Algorithms (Computational Molecular Biology).","author":"Jones","year":"2004"},{"key":"2023012512021304400_B7","doi-asserted-by":"crossref","first-page":"R116","DOI":"10.1186\/gb-2010-11-11-r116","article-title":"Quake: quality-aware detection and correction of sequencing errors","volume":"11","author":"Kelley","year":"2010","journal-title":"Genome Biol."},{"key":"2023012512021304400_B8","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1007\/s00253-006-0725-7","article-title":"Specific single-cell isolation and genomic amplification of uncultured microorganisms","volume":"74","author":"Kvist","year":"2007","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"2023012512021304400_B9","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2023012512021304400_B10","doi-asserted-by":"crossref","first-page":"R50","DOI":"10.1186\/gb-2010-11-5-r50","article-title":"Modeling non-uniformity in short-read rates in rna-seq data","volume":"11","author":"Li","year":"2010","journal-title":"Genome Biol."},{"key":"2023012512021304400_B11","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1093\/bioinformatics\/18.3.440","article-title":"PatternHunter: faster and more sensitive homology search","volume":"18","author":"Ma","year":"2002","journal-title":"Bioinformatics"},{"key":"2023012512021304400_B12","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature03959","article-title":"Genome sequencing in microfabricated high-density picolitre reactors","volume":"437","author":"Margulies","year":"2005","journal-title":"Nature"},{"key":"2023012512021304400_B13","doi-asserted-by":"crossref","first-page":"e230","DOI":"10.1371\/journal.pbio.0050230","article-title":"Insights into the genome of large sulfur bacteria revealed by analysis of single filaments","volume":"5","author":"Mussmann","year":"2007","journal-title":"PLoS Biol."},{"key":"2023012512021304400_B14","doi-asserted-by":"crossref","first-page":"9748","DOI":"10.1073\/pnas.171285098","article-title":"An Eulerian path approach to DNA fragment assembly","volume":"98","author":"Pevzner","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012512021304400_B15","doi-asserted-by":"crossref","first-page":"1309","DOI":"10.1101\/gr.089151.108","article-title":"Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing","volume":"19","author":"Qu","year":"2009","journal-title":"Genome Res."},{"key":"2023012512021304400_B16","doi-asserted-by":"crossref","first-page":"3342","DOI":"10.1128\/AEM.71.6.3342-3347.2005","article-title":"Genomic DNA amplification from a single bacterium","volume":"71","author":"Raghunathan","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"2023012512021304400_B17","doi-asserted-by":"crossref","first-page":"e6864","DOI":"10.1371\/journal.pone.0006864","article-title":"Whole genome amplification and de novo assembly of single bacterial cells","volume":"4","author":"Rodrigue","year":"2009","journal-title":"PLoS ONE"},{"key":"2023012512021304400_B18","doi-asserted-by":"crossref","first-page":"1284","DOI":"10.1093\/bioinformatics\/btq151","article-title":"Correction of sequencing errors in a mixed set of reads","volume":"26","author":"Salmela","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512021304400_B19","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1093\/bioinformatics\/btp379","article-title":"SHREC: a short-read error correction method","volume":"25","author":"Schroder","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512021304400_B20","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1089\/cmb.2009.0062","article-title":"A parallel algorithm for error correction in high-throughput short-read data on cuda-enabled graphics hardware","volume":"17","author":"Shi","year":"2010","journal-title":"J. Comput. Biol."},{"key":"2023012512021304400_B21","first-page":"189","article-title":"Recount: expectation maximization based error correction tool for next generation sequencing data","volume":"23","author":"Wijaya","year":"2009","journal-title":"Genome Inform. Ser."},{"key":"2023012512021304400_B22","doi-asserted-by":"crossref","first-page":"2526","DOI":"10.1093\/bioinformatics\/btq468","article-title":"Reptile: representative tiling for short read error correction","volume":"26","author":"Yang","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512021304400_B23","doi-asserted-by":"crossref","first-page":"e16","DOI":"10.1371\/journal.pbio.0050016","article-title":"The sorcerer iiglobal ocean sampling expedition: Expanding the universe of protein families","volume":"5","author":"Yooseph","year":"2007","journal-title":"PLoS Biol."},{"key":"2023012512021304400_B24","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for de novo short read assembly using de Bruijn graphs","volume":"18","author":"Zerbino","year":"2008","journal-title":"Genome Res."},{"key":"2023012512021304400_B25","doi-asserted-by":"crossref","first-page":"1549","DOI":"10.1089\/cmb.2010.0127","article-title":"Edar: an efficient error detection and removal algorithm for next generation sequencing data","volume":"17","author":"Zhao","year":"2010","journal-title":"J. Comput. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/13\/i137\/48874088\/bioinformatics_27_13_i137.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/13\/i137\/48874088\/bioinformatics_27_13_i137.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T14:21:22Z","timestamp":1674656482000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/13\/i137\/178096"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,6,14]]},"references-count":25,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2011,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr208","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,7,1]]},"published":{"date-parts":[[2011,6,14]]}}}