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Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>PANDAseq assembles paired-end reads rapidly and with the correction of most errors. Uncertain error corrections come from reads with many low-quality bases identified by upstream processing. Benchmarks were done using real error masks on simulated data, a pure source template, and a pooled template of genomic DNA from known organisms. PANDAseq assembled reads more rapidly and with reduced error incorporation compared to alternative methods.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>PANDAseq rapidly assembles sequences and scales to billions of paired-end reads. Assembly of control libraries showed a 4-50% increase in the number of assembled sequences over na\u00efve assembly with negligible loss of \"good\" sequence.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-13-31","type":"journal-article","created":{"date-parts":[[2012,2,14]],"date-time":"2012-02-14T13:14:14Z","timestamp":1329225254000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1853,"title":["PANDAseq: paired-end assembler for illumina sequences"],"prefix":"10.1186","volume":"13","author":[{"given":"Andre P","family":"Masella","sequence":"first","affiliation":[]},{"given":"Andrea K","family":"Bartram","sequence":"additional","affiliation":[]},{"given":"Jakub M","family":"Truszkowski","sequence":"additional","affiliation":[]},{"given":"Daniel G","family":"Brown","sequence":"additional","affiliation":[]},{"given":"Josh D","family":"Neufeld","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,2,14]]},"reference":[{"key":"5124_CR1","doi-asserted-by":"publisher","first-page":"3846","DOI":"10.1128\/AEM.02772-10","volume":"77","author":"AK Bartram","year":"2011","unstructured":"Bartram AK, Lynch MDJ, Stearns JC, Moreno-Hagelsieb G, Neufeld JD: Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads. 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