{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,30]],"date-time":"2025-12-30T03:44:06Z","timestamp":1767066246914},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Ultra-high-throughput sequencing produces duplicate and near-duplicate reads, which can consume computational resources in downstream applications. A tool that collapses such reads should reduce storage and assembly complications and costs.<\/jats:p>\n               <jats:p>Results: We developed Fulcrum to collapse identical and near-identical Illumina and 454 reads (such as those from PCR clones) into single error-corrected sequences; it can process paired-end as well as single-end reads. Fulcrum is customizable and can be deployed on a single machine, a local network or a commercially available MapReduce cluster, and it has been optimized to maximize ease-of-use, cross-platform compatibility and future scalability. Sequence datasets have been collapsed by up to 71%, and the reduced number and improved quality of the resulting sequences allow assemblers to produce longer contigs while using less memory.<\/jats:p>\n               <jats:p>Availability and implementation: Source code and a tutorial are available at http:\/\/pringlelab.stanford.edu\/protocols.html under a BSD-like license. Fulcrum was written and tested in Python 2.6, and the single-machine and local-network modes depend on a modified version of the Parallel Python library (provided).<\/jats:p>\n               <jats:p>Contact: \u00a0erik.m.lehnert@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary information is available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts123","type":"journal-article","created":{"date-parts":[[2012,3,15]],"date-time":"2012-03-15T05:33:56Z","timestamp":1331789636000},"page":"1324-1327","source":"Crossref","is-referenced-by-count":35,"title":["Fulcrum: condensing redundant reads from high-throughput sequencing studies"],"prefix":"10.1093","volume":"28","author":[{"given":"Matthew S.","family":"Burriesci","sequence":"first","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA"}]},{"given":"Erik M.","family":"Lehnert","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA"}]},{"given":"John R.","family":"Pringle","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,3,13]]},"reference":[{"key":"2023012512302521400_B1","doi-asserted-by":"crossref","first-page":"S6","DOI":"10.1038\/nmeth.1376","article-title":"Sense from sequence reads: methods for alignment and assembly","volume":"6","author":"Flicek","year":"2009","journal-title":"Nat. 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