{"id":"https://openalex.org/W3042808865","doi":"https://doi.org/10.1186/s12859-020-03649-5","title":"PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST","display_name":"PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST","publication_year":2020,"publication_date":"2020-07-16","ids":{"openalex":"https://openalex.org/W3042808865","doi":"https://doi.org/10.1186/s12859-020-03649-5","mag":"3042808865","pmid":"https://pubmed.ncbi.nlm.nih.gov/32677886"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-03649-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03649-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-03649-5","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/s12859-020-03649-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063125477","display_name":"Cinque Soto","orcid":"https://orcid.org/0000-0002-3997-6217"},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cinque Soto","raw_affiliation_strings":["Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA","Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I901861585"]},{"raw_affiliation_string":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056521552","display_name":"Jessica A. Finn","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jessica A. Finn","raw_affiliation_strings":["Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, 37232, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019038548","display_name":"Jordan R. Willis","orcid":"https://orcid.org/0000-0002-0135-5263"},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jordan R. Willis","raw_affiliation_strings":["Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000578394","display_name":"Samuel B. Day","orcid":null},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samuel B. Day","raw_affiliation_strings":["Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071084715","display_name":"Robert S. Sinkovits","orcid":"https://orcid.org/0000-0001-7377-9762"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert S. Sinkovits","raw_affiliation_strings":["San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, 92093, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, 92093, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077409882","display_name":"Taylor Jones","orcid":"https://orcid.org/0000-0002-8591-2847"},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Taylor Jones","raw_affiliation_strings":["Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060262479","display_name":"Samuel Schmitz","orcid":"https://orcid.org/0000-0001-5314-6095"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samuel Schmitz","raw_affiliation_strings":["Department of Chemistry, Vanderbilt University, Nashville, TN, 37212, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Vanderbilt University, Nashville, TN, 37212, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025842562","display_name":"Jens Meiler","orcid":"https://orcid.org/0000-0001-8945-193X"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jens Meiler","raw_affiliation_strings":["Department of Chemistry, Vanderbilt University, Nashville, TN, 37212, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Vanderbilt University, Nashville, TN, 37212, USA","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000470565","display_name":"Andre Branchizio","orcid":null},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andre Branchizio","raw_affiliation_strings":["Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046971682","display_name":"James E. Crowe","orcid":"https://orcid.org/0000-0002-0049-1079"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]},{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"James E. Crowe","raw_affiliation_strings":["Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, 37232, USA. james.crowe@vumc.org","Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA. james.crowe@vumc.org","Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA. james.crowe@vumc.org","Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, 37232, USA"],"raw_orcid":"https://orcid.org/0000-0002-0049-1079","affiliations":[{"raw_affiliation_string":"Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, 37232, USA. james.crowe@vumc.org","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA. james.crowe@vumc.org","institution_ids":["https://openalex.org/I901861585"]},{"raw_affiliation_string":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA. james.crowe@vumc.org","institution_ids":["https://openalex.org/I901861585"]},{"raw_affiliation_string":"Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, 37232, USA","institution_ids":["https://openalex.org/I200719446"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5046971682"],"corresponding_institution_ids":["https://openalex.org/I200719446","https://openalex.org/I901861585"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.8148,"has_fulltext":true,"cited_by_count":34,"citation_normalized_percentile":{"value":0.92621188,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"21","issue":"1","first_page":"314","last_page":"314"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.6270999908447266,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.6270999908447266,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.1590999960899353,"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.13230000436306,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.756832480430603},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6615909337997437},{"id":"https://openalex.org/keywords/json","display_name":"JSON","score":0.6563677191734314},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5779548287391663},{"id":"https://openalex.org/keywords/chunking","display_name":"Chunking (psychology)","score":0.5731266736984253},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.571983277797699},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5719025135040283},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.410054087638855},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33267277479171753},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3193802833557129},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.27594050765037537},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.25016355514526367},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22359833121299744},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.15103289484977722},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12203177809715271},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11263898015022278}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.756832480430603},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6615909337997437},{"id":"https://openalex.org/C2780416260","wikidata":"https://www.wikidata.org/wiki/Q2063","display_name":"JSON","level":2,"score":0.6563677191734314},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5779548287391663},{"id":"https://openalex.org/C203357204","wikidata":"https://www.wikidata.org/wiki/Q1089605","display_name":"Chunking (psychology)","level":2,"score":0.5731266736984253},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.571983277797699},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5719025135040283},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.410054087638855},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33267277479171753},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3193802833557129},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.27594050765037537},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.25016355514526367},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22359833121299744},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.15103289484977722},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12203177809715271},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11263898015022278}],"mesh":[{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-020-03649-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03649-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-03649-5","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:32677886","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32677886","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:doaj.org/article:edd5c95dc07b4be798f44bcf7e346469","is_oa":true,"landing_page_url":"https://doaj.org/article/edd5c95dc07b4be798f44bcf7e346469","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 21, Iss 1, Pp 1-7 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7364545","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7364545","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"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-03649-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03649-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-03649-5","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":[],"awards":[{"id":"https://openalex.org/G1611379837","display_name":null,"funder_award_id":"HHSN272201400024C","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G215535693","display_name":null,"funder_award_id":"U19 AI117905","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3539628403","display_name":null,"funder_award_id":"HHSN272201400024C","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3917909134","display_name":null,"funder_award_id":"U19 AI117905","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6286301463","display_name":null,"funder_award_id":"AI117905","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320317977","display_name":"Human Vaccines Project","ror":"https://ror.org/02jkp0740"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3042808865.pdf","grobid_xml":"https://content.openalex.org/works/W3042808865.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W135571511","https://openalex.org/W1982828034","https://openalex.org/W2022824615","https://openalex.org/W2029525307","https://openalex.org/W2055043387","https://openalex.org/W2084390276","https://openalex.org/W2101375662","https://openalex.org/W2151558930","https://openalex.org/W2340112726","https://openalex.org/W2565989705","https://openalex.org/W2581134553","https://openalex.org/W2910384850","https://openalex.org/W2911840537","https://openalex.org/W2911980279","https://openalex.org/W2979751218","https://openalex.org/W2997321681"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2753132265","https://openalex.org/W4234766820","https://openalex.org/W4321232174","https://openalex.org/W3117520771","https://openalex.org/W2482048793","https://openalex.org/W4388027365","https://openalex.org/W2938860153","https://openalex.org/W4312551432","https://openalex.org/W2365783963"],"abstract_inverted_index":{"BACKGROUND:":[0],"Recent":[1],"advances":[2],"in":[3,11,27,52,142],"DNA":[4,18],"sequencing":[5],"technologies":[6],"have":[7,59],"enabled":[8],"significant":[9],"leaps":[10],"capacity":[12],"to":[13,124,127,139],"generate":[14],"large":[15,82],"volumes":[16],"of":[17,30,35,46,131],"sequence":[19,83,92],"data,":[20],"which":[21,69],"has":[22],"spurred":[23],"a":[24,33,62,71,112,128],"rapid":[25],"growth":[26],"the":[28],"use":[29],"bioinformatics":[31,144],"as":[32],"means":[34],"interrogating":[36],"antibody":[37,47],"variable":[38],"gene":[39],"repertoires.":[40],"Common":[41],"tools":[42],"used":[43,141],"for":[44,67,81,137],"annotation":[45],"sequences":[48],"are":[49],"often":[50],"limited":[51],"functionality,":[53],"modularity":[54],"and":[55,65,75,86,90,119],"usability.":[56],"RESULTS:":[57],"We":[58],"developed":[60],"PyIR,":[61],"Python":[63,87],"wrapper":[64],"library":[66],"IgBLAST,":[68],"offers":[70,96],"minimal":[72],"setup":[73],"CLI":[74],"API,":[76],"FASTQ":[77],"support,":[78],"file":[79],"chunking":[80],"files,":[84],"JSON":[85],"dictionary":[88],"output,":[89],"built-in":[91],"filtering.":[93],"CONCLUSIONS:":[94],"PyIR":[95],"improved":[97],"processing":[98],"speed":[99],"over":[100],"multithreaded":[101],"IgBLAST":[102,138],"(version":[103],"1.14)":[104],"when":[105],"spawning":[106],"more":[107],"than":[108],"16":[109],"processes":[110],"on":[111],"single":[113],"computer":[114],"system.":[115],"Its":[116],"customizable":[117],"filtering":[118],"data":[120],"encapsulation":[121],"allow":[122],"it":[123],"be":[125,140],"adapted":[126],"wide":[129],"range":[130],"computing":[132],"environments.":[133],"The":[134],"API":[135],"allows":[136],"customized":[143],"workflows.":[145]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":4}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
