{"id":"https://openalex.org/W2152124936","doi":"https://doi.org/10.1186/1471-2105-13-297","title":"Oculus: faster sequence alignment by streaming read compression","display_name":"Oculus: faster sequence alignment by streaming read compression","publication_year":2012,"publication_date":"2012-11-13","ids":{"openalex":"https://openalex.org/W2152124936","doi":"https://doi.org/10.1186/1471-2105-13-297","mag":"2152124936","pmid":"https://pubmed.ncbi.nlm.nih.gov/23148484"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-297","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-297","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-297","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-297","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023147760","display_name":"Brendan Veeneman","orcid":"https://orcid.org/0000-0002-2371-2815"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brendan A Veeneman","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA","Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109589456","display_name":"Matthew K. Iyer","orcid":"https://orcid.org/0000-0002-0217-7390"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210117557","display_name":"Michigan Center for Translational Pathology","ror":"https://ror.org/027t4kk23","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210114445","https://openalex.org/I4210117557"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew K Iyer","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA","Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210117557"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003311852","display_name":"Arul M. Chinnaiyan","orcid":"https://orcid.org/0000-0001-9282-3415"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210117557","display_name":"Michigan Center for Translational Pathology","ror":"https://ror.org/027t4kk23","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210114445","https://openalex.org/I4210117557"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Arul M Chinnaiyan","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA","Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA","Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA","Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, 48109, USA","Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I27837315"]},{"raw_affiliation_string":"Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210117557"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5003311852"],"corresponding_institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I27837315","https://openalex.org/I4210117557"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.3684,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.60030484,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"13","issue":"1","first_page":"297","last_page":"297"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9754999876022339,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9754999876022339,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.004000000189989805,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.0024999999441206455,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8696731328964233},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.7183592319488525},{"id":"https://openalex.org/keywords/redundancy","display_name":"Redundancy (engineering)","score":0.5919985175132751},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4487893283367157},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.44826751947402954},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.4439485967159271},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.22075852751731873},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.19021961092948914},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.16759687662124634}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8696731328964233},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.7183592319488525},{"id":"https://openalex.org/C152124472","wikidata":"https://www.wikidata.org/wiki/Q1204361","display_name":"Redundancy (engineering)","level":2,"score":0.5919985175132751},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4487893283367157},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.44826751947402954},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.4439485967159271},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.22075852751731873},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.19021961092948914},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.16759687662124634},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-13-297","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-297","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-297","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23148484","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23148484","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:deepblue.lib.umich.edu:2027.42/112673","is_oa":true,"landing_page_url":"https://hdl.handle.net/2027.42/112673","pdf_url":"https://hdl.handle.net/2027.42/112673","source":{"id":"https://openalex.org/S4306400393","display_name":"Deep Blue (University of Michigan)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I27837315","host_organization_name":"University of Michigan","host_organization_lineage":["https://openalex.org/I27837315"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:europepmc.org:2537163","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3534618","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3534618","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3534618","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:dbab99e1a57f40d5a7ab49cae3566c8c","is_oa":false,"landing_page_url":"https://doaj.org/article/dbab99e1a57f40d5a7ab49cae3566c8c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 13, Iss 1, p 297 (2012)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-297","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-297","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-297","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.47999998927116394,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306078","display_name":"U.S. Department of Defense","ror":"https://ror.org/0447fe631"},{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320309652","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2152124936.pdf","grobid_xml":"https://content.openalex.org/works/W2152124936.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W2000586119","https://openalex.org/W2005112508","https://openalex.org/W2006559366","https://openalex.org/W2017928178","https://openalex.org/W2055043387","https://openalex.org/W2087064593","https://openalex.org/W2097065948","https://openalex.org/W2103441770","https://openalex.org/W2105765411","https://openalex.org/W2112113834","https://openalex.org/W2121762798","https://openalex.org/W2124985265","https://openalex.org/W2141978878","https://openalex.org/W2155266131","https://openalex.org/W2158714788","https://openalex.org/W2163871842","https://openalex.org/W2168303240","https://openalex.org/W2247766769"],"related_works":["https://openalex.org/W1657880117","https://openalex.org/W2595172197","https://openalex.org/W2135248929","https://openalex.org/W2092690310","https://openalex.org/W1493624592","https://openalex.org/W3190662310","https://openalex.org/W2794767707","https://openalex.org/W1507878993","https://openalex.org/W2798440551","https://openalex.org/W2888459714"],"abstract_inverted_index":{"BACKGROUND:":[0],"Despite":[1],"significant":[2],"advancement":[3],"in":[4,37,67,150,173],"alignment":[5,29,48,54,106,144],"algorithms,":[6],"the":[7,22,68,151,177,203],"exponential":[8],"growth":[9],"of":[10,24,95,108,115,123,176,184],"nucleotide":[11],"sequencing":[12],"throughput":[13,154],"threatens":[14],"to":[15,63,81,105,110,139,167,202],"outpace":[16],"bioinformatic":[17],"analysis.":[18],"Computation":[19],"may":[20],"become":[21,135],"bottleneck":[23],"genome":[25],"analysis":[26],"if":[27],"growing":[28],"costs":[30],"are":[31,61],"not":[32],"mitigated":[33],"by":[34,88],"further":[35],"improvement":[36],"algorithms.":[38],"Much":[39],"gain":[40],"has":[41],"been":[42],"gleaned":[43],"from":[44],"indexing":[45],"and":[46,60,84,93,142,146,163,191,200],"compressing":[47],"databases,":[49],"but":[50],"many":[51],"widely":[52],"used":[53],"tools":[55],"process":[56,101],"input":[57,96,161],"reads":[58,69,162],"sequentially":[59],"oblivious":[62],"any":[64],"underlying":[65],"redundancy":[66,87],"themselves.":[70],"RESULTS:":[71],"Here":[72],"we":[73],"present":[74],"Oculus,":[75],"a":[76,113,120,136,174,182],"software":[77],"package":[78],"that":[79,127],"attaches":[80],"standard":[82,137],"aligners":[83,166],"exploits":[85],"read":[86,129],"performing":[89],"streaming":[90,128],"compression,":[91],"alignment,":[92],"decompression":[94],"sequences.":[97],"This":[98],"nearly":[99,169],"lossless":[100],"(>":[102],"99.9%)":[103],"led":[104],"speedups":[107],"up":[109],"270%":[111],"across":[112],"variety":[114],"data":[116],"sets,":[117],"while":[118],"requiring":[119],"modest":[121],"amount":[122],"memory.":[124],"We":[125],"expect":[126],"compressors":[130],"such":[131,187],"as":[132,153,188],"Oculus":[133,157],"could":[134],"addition":[138],"existing":[140,165],"RNA-Seq":[141],"ChIP-Seq":[143],"pipelines,":[145],"potentially":[147],"other":[148],"applications":[149],"future":[152],"increases.":[155],"CONCLUSIONS:":[156],"efficiently":[158],"condenses":[159],"redundant":[160],"wraps":[164],"provide":[168],"identical":[170],"SAM":[171,204],"output":[172],"fraction":[175],"aligner":[178],"runtime.":[179],"It":[180],"includes":[181],"number":[183],"useful":[185],"features,":[186],"tunable":[189],"performance":[190],"fidelity":[192],"options,":[193],"compatibility":[194],"with":[195],"FASTA":[196],"or":[197],"FASTQ":[198],"files,":[199],"adherence":[201],"format.":[205],"The":[206],"platform-independent":[207],"C++":[208],"source":[209],"code":[210],"is":[211],"freely":[212],"available":[213],"online,":[214],"at":[215],"http://code.google.com/p/oculus-bio.":[216]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":3}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
