{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T07:03:12Z","timestamp":1761807792119},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Next-generation sequence analysis has become an important task both in laboratory and clinical settings. A key stage in the majority sequence analysis workflows, such as resequencing, is the alignment of genomic reads to a reference genome. The accurate alignment of reads with large indels is a computationally challenging task for researchers.<\/jats:p>\n               <jats:p>Results: We introduce SeqAlto as a new algorithm for read alignment. For reads longer than or equal to 100 bp, SeqAlto is up to 10 \u00d7 faster than existing algorithms, while retaining high accuracy and the ability to align reads with large (up to 50 bp) indels. This improvement in efficiency is particularly important in the analysis of future sequencing data where the number of reads approaches many billions. Furthermore, SeqAlto uses less than 8 GB of memory to align against the human genome. SeqAlto is benchmarked against several existing tools with both real and simulated data.<\/jats:p>\n               <jats:p>Availability: Linux and Mac OS X binaries free for academic use are available at http:\/\/www.stanford.edu\/group\/wonglab\/seqalto<\/jats:p>\n               <jats:p>Contact: \u00a0whwong@stanford.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts450","type":"journal-article","created":{"date-parts":[[2012,7,19]],"date-time":"2012-07-19T11:38:30Z","timestamp":1342697910000},"page":"2366-2373","source":"Crossref","is-referenced-by-count":43,"title":["Fast and accurate read alignment for resequencing"],"prefix":"10.1093","volume":"28","author":[{"given":"John C.","family":"Mu","sequence":"first","affiliation":[{"name":"1 Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA, 2Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA, 3Bina Technologies Inc., Redwood City and 4Department of Statistics, Stanford University, Stanford, CA 94305, USA"}]},{"given":"Hui","family":"Jiang","sequence":"additional","affiliation":[{"name":"1 Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA, 2Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA, 3Bina Technologies Inc., Redwood City and 4Department of Statistics, Stanford University, Stanford, CA 94305, USA"}]},{"given":"Amirhossein","family":"Kiani","sequence":"additional","affiliation":[{"name":"1 Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA, 2Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA, 3Bina Technologies Inc., Redwood City and 4Department of Statistics, Stanford University, Stanford, CA 94305, USA"}]},{"given":"Marghoob","family":"Mohiyuddin","sequence":"additional","affiliation":[{"name":"1 Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA, 2Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA, 3Bina Technologies Inc., Redwood City and 4Department of Statistics, Stanford University, Stanford, CA 94305, USA"}]},{"given":"Narges","family":"Bani Asadi","sequence":"additional","affiliation":[{"name":"1 Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA, 2Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA, 3Bina Technologies Inc., Redwood City and 4Department of Statistics, Stanford University, Stanford, CA 94305, USA"}]},{"given":"Wing H.","family":"Wong","sequence":"additional","affiliation":[{"name":"1 Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA, 2Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA, 3Bina Technologies Inc., Redwood City and 4Department of Statistics, Stanford University, Stanford, CA 94305, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,7,18]]},"reference":[{"key":"2023012513005649200_bts450-B1","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1007\/3-540-56024-6_15","article-title":"Fast and practical approximate string matching","volume-title":"Combinatorial Pattern Matching, Third Annual Symposium","author":"Baeza-yates","year":"1992"},{"key":"2023012513005649200_bts450-B2","article-title":"A block-sorting lossless data compression algorithm","author":"Burrows","year":"1994","journal-title":"HP Labs Technical Reports, SRC-RR-124"},{"key":"2023012513005649200_bts450-B3","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1093\/bioinformatics\/btr046","article-title":"SHRiMP2: sensitive yet practical short read mapping","volume":"27","author":"David","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012513005649200_bts450-B4","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation dna sequencing data","volume":"43","author":"DePristo","year":"2011","journal-title":"Nat. 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