{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T10:47:39Z","timestamp":1761648459818,"version":"3.28.0"},"reference-count":31,"publisher":"IEEE","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,5]]},"DOI":"10.1109\/ipdps.2017.35","type":"proceedings-article","created":{"date-parts":[[2017,7,3]],"date-time":"2017-07-03T20:41:58Z","timestamp":1499114518000},"page":"52-61","source":"Crossref","is-referenced-by-count":4,"title":["PUNAS: A Parallel Ungapped-Alignment-Featured Seed Verification Algorithm for Next-Generation Sequencing Read Alignment"],"prefix":"10.1109","author":[{"given":"Yuandong","family":"Chan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai","family":"Xu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haidong","family":"Lan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weiguo","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yongchao","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bertil","family":"Schmidt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"263","reference":[{"year":"0","key":"ref31"},{"key":"ref30","first-page":"11","volume":"9","author":"d\u00f6ring","year":"2008","journal-title":"SeqAn an efficient generic C++ library for sequence analysis BMC Bioinformatics"},{"key":"ref10","volume":"9","author":"liu","year":"2014","journal-title":"CUSHAW3 Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding PLoS One"},{"key":"ref11","first-page":"1185","volume":"9","author":"marco-sola","year":"2012","journal-title":"The GEM mapper fast accurate and versatile alignment by filtration Nature Methods"},{"key":"ref12","volume":"41","author":"siragusa","year":"2013","journal-title":"Fast and accurate read mapping with approximate seeds and multiple backtracking Nucleic Acids Research"},{"key":"ref13","volume":"16","author":"cheng","year":"2015","journal-title":"an efficient all-mapper based on bit-vector computing BMC Bioinformatics"},{"key":"ref14","first-page":"1061","volume":"41","author":"alkan","year":"2009","journal-title":"Personalized copy number and segmental duplication maps using next-generation sequencing Nature Genetics"},{"key":"ref15","first-page":"53","volume":"2","author":"abouelhoda","year":"2014","journal-title":"Replacing suffix trees with enhanced suffix arrays Journal of Discrete Algorithms"},{"key":"ref16","volume":"52","author":"ferragina","year":"2005","journal-title":"Indexing Compressed Text Journal of the ACM"},{"key":"ref17","first-page":"156","volume":"23","author":"farrar","year":"2007","journal-title":"Striped Smith-Waterman speeds database searches six times over other SIMD implementations Bioinformatics"},{"key":"ref18","volume":"14(sl)","author":"xin","year":"2013","journal-title":"Accelerating read mapping with FastHash BMC Genomics"},{"key":"ref19","first-page":"4003","volume":"31","author":"abun","year":"2015","journal-title":"BigBWA approaching the Burrows-Wheeler aligner to Big Data technologies Bioinformatics"},{"key":"ref28","volume":"8","author":"zhao","year":"2013","journal-title":"Ssw library An simd smith-waterman c\/c++ library for use in genomic applications"},{"key":"ref4","first-page":"2592","author":"weese","year":"2012","journal-title":"RazerS3 faster fully sensitive read mapping Bioinformatics 28 20"},{"journal-title":"Mason - A read simulator for second generation sequencing data Technical Report FU Berlin","year":"2010","author":"holtgrewe","key":"ref27"},{"journal-title":"Short Read Mapping An Algorithmic Tour Proceedings of the IEEE in Press","year":"2016","author":"canzar","key":"ref3"},{"key":"ref6","volume":"46","author":"myers","year":"1999","journal-title":"A fast Bit-Vector algorithm for approximate string matching based on dynamic programming Journal of the ACM"},{"key":"ref29","volume":"9","author":"lee","year":"2014","journal-title":"MOSAIK a hash-based algorithm for accurate next-generation sequencing short-read mapping PloS ONE"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"smith","year":"1981","journal-title":"Identication of Common Molecular Subsequences Journal of Molecular Biology"},{"journal-title":"Aligning Sequence Reads Clone Sequences and Assembly Contigs with BWA-MEM","year":"2013","author":"li","key":"ref8"},{"key":"ref7","first-page":"1553","volume":"31","author":"xin","year":"2015","journal-title":"Shifted Hamming distance a fast and accurate SIMD- friendly filter to accelerate alignment verification in read mapping Bioinformatics"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1146\/annurev-genom-090413-025358","volume":"16","author":"reinert","year":"2015","journal-title":"Alignment of Next-Generation Sequencing Reads Annual Review of Genomics and Human Genetics"},{"key":"ref9","volume":"9","author":"langmead","year":"2012","journal-title":"Fast gapped-read alignment with Bowtie 2 Nature Methods"},{"key":"ref1","first-page":"1002195e","volume":"13","author":"stephens","year":"2015","journal-title":"Big Data Astronomical or Genomical? PLoS BioI"},{"journal-title":"parSRA A framework for the parallel execution of short read aligners on compute clusters Journal of Computational Science","year":"2017","author":"gonzalez-dominguez","key":"ref20"},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.1109\/SAMOS.2015.7363679"},{"key":"ref21","first-page":"1830","volume":"28","author":"liu","year":"2012","journal-title":"CUSHAW a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform Bioinformatics"},{"key":"ref24","volume":"3 e808","author":"wilton","year":"2015","journal-title":"Arioc high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space PeerJ"},{"journal-title":"meraligner A fully parallel sequence aligner In Proceedings of the IPDPS IEEE Press","year":"2015","author":"georganas","key":"ref23"},{"journal-title":"GateKeeper Enabling Fast Pre-Alignment in DNA Short Read Mapping with a New Streaming Accelerator Architecture","year":"2016","author":"alser","key":"ref26"},{"key":"ref25","volume":"s10","author":"luo","year":"2015","journal-title":"MICA A fast short-read aligner that takes full advantage of Many Integrated Core Architecture BMC Bioinformatics 16(Suppl7)"}],"event":{"name":"2017 IEEE International Parallel and Distributed Processing Symposium (IPDPS)","start":{"date-parts":[[2017,5,29]]},"location":"Orlando, FL, USA","end":{"date-parts":[[2017,6,2]]}},"container-title":["2017 IEEE International Parallel and Distributed Processing Symposium (IPDPS)"],"original-title":[],"link":[{"URL":"http:\/\/xplorestaging.ieee.org\/ielx7\/7965806\/7967079\/07967095.pdf?arnumber=7967095","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,10,11]],"date-time":"2020-10-11T12:36:43Z","timestamp":1602419803000},"score":1,"resource":{"primary":{"URL":"http:\/\/ieeexplore.ieee.org\/document\/7967095\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,5]]},"references-count":31,"URL":"https:\/\/doi.org\/10.1109\/ipdps.2017.35","relation":{},"subject":[],"published":{"date-parts":[[2017,5]]}}}