{"id":"https://openalex.org/W2761002607","doi":"https://doi.org/10.1186/s12859-017-1853-z","title":"VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data","display_name":"VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data","publication_year":2017,"publication_date":"2017-10-11","ids":{"openalex":"https://openalex.org/W2761002607","doi":"https://doi.org/10.1186/s12859-017-1853-z","mag":"2761002607","pmid":"https://pubmed.ncbi.nlm.nih.gov/29020925"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-017-1853-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1853-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1853-z","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/track/pdf/10.1186/s12859-017-1853-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078078996","display_name":"Scott Christley","orcid":"https://orcid.org/0000-0002-9889-1221"},"institutions":[{"id":"https://openalex.org/I4388891891","display_name":"Southwestern Medical Center","ror":"https://ror.org/05d80e146","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I4388891891"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott Christley","raw_affiliation_strings":["Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA","institution_ids":["https://openalex.org/I4388891891","https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024040294","display_name":"Mikhail K. Levin","orcid":null},"institutions":[{"id":"https://openalex.org/I100621029","display_name":"Bank of America","ror":"https://ror.org/006tvg625","country_code":"US","type":"other","lineage":["https://openalex.org/I100621029"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mikhail K. Levin","raw_affiliation_strings":["Bank of America Corporate Center, Charlotte, NC, 28202, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bank of America Corporate Center, Charlotte, NC, 28202, USA","institution_ids":["https://openalex.org/I100621029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030533815","display_name":"Inimary T. Toby","orcid":"https://orcid.org/0000-0003-0820-3999"},"institutions":[{"id":"https://openalex.org/I4388891891","display_name":"Southwestern Medical Center","ror":"https://ror.org/05d80e146","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I4388891891"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Inimary T. Toby","raw_affiliation_strings":["Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA","institution_ids":["https://openalex.org/I4388891891","https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051814524","display_name":"John Fonner","orcid":"https://orcid.org/0000-0003-4398-2916"},"institutions":[{"id":"https://openalex.org/I4388891828","display_name":"Texas Advanced Computing Center","ror":"https://ror.org/00xg4bh43","country_code":null,"type":"facility","lineage":["https://openalex.org/I4388891828","https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John M. Fonner","raw_affiliation_strings":["Texas Advanced Computing Center, Austin, TX, 78758-4497, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Texas Advanced Computing Center, Austin, TX, 78758-4497, USA","institution_ids":["https://openalex.org/I4388891828"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109079767","display_name":"Nancy Monson","orcid":null},"institutions":[{"id":"https://openalex.org/I4388891891","display_name":"Southwestern Medical Center","ror":"https://ror.org/05d80e146","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I4388891891"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nancy L. Monson","raw_affiliation_strings":["Department of Immunology, UT Southwestern Medical Center, Dallas, TX, 75390, USA","Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, Dallas, TX, 75390, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Immunology, UT Southwestern Medical Center, Dallas, TX, 75390, USA","institution_ids":["https://openalex.org/I4388891891","https://openalex.org/I867280407"]},{"raw_affiliation_string":"Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, Dallas, TX, 75390, USA","institution_ids":["https://openalex.org/I4388891891","https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029755765","display_name":"William Rounds","orcid":null},"institutions":[{"id":"https://openalex.org/I4388891891","display_name":"Southwestern Medical Center","ror":"https://ror.org/05d80e146","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I4388891891"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William H. Rounds","raw_affiliation_strings":["Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA","institution_ids":["https://openalex.org/I4388891891","https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112258904","display_name":"Florian Rubelt","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Florian Rubelt","raw_affiliation_strings":["Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054148594","display_name":"Walter Scarborough","orcid":null},"institutions":[{"id":"https://openalex.org/I4388891828","display_name":"Texas Advanced Computing Center","ror":"https://ror.org/00xg4bh43","country_code":null,"type":"facility","lineage":["https://openalex.org/I4388891828","https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Walter Scarborough","raw_affiliation_strings":["Texas Advanced Computing Center, Austin, TX, 78758-4497, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Texas Advanced Computing Center, Austin, TX, 78758-4497, USA","institution_ids":["https://openalex.org/I4388891828"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034262562","display_name":"Richard H. Scheuermann","orcid":"https://orcid.org/0000-0003-1355-892X"},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]},{"id":"https://openalex.org/I1311191458","display_name":"La Jolla Institute for Immunology","ror":"https://ror.org/05vkpd318","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1311191458"]},{"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":"Richard H. Scheuermann","raw_affiliation_strings":["Department of Pathology, University of California, San Diego, CA, 92093, USA","J. Craig Venter Institute, La Jolla, CA, 92037, USA","La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, University of California, San Diego, CA, 92093, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"J. Craig Venter Institute, La Jolla, CA, 92037, USA","institution_ids":["https://openalex.org/I1301553790"]},{"raw_affiliation_string":"La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA","institution_ids":["https://openalex.org/I1311191458"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090203652","display_name":"Lindsay G. Cowell","orcid":"https://orcid.org/0000-0003-1617-8244"},"institutions":[{"id":"https://openalex.org/I4210096815","display_name":"Southwestern Medical Center","ror":"https://ror.org/00t9vx427","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210096815"]},{"id":"https://openalex.org/I4388891891","display_name":"Southwestern Medical Center","ror":"https://ror.org/05d80e146","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I4388891891"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lindsay G. Cowell","raw_affiliation_strings":["Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA. lindsay.cowell@utsouthwestern.edu","Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA. lindsay.cowell@utsouthwestern.edu","institution_ids":["https://openalex.org/I4210096815","https://openalex.org/I867280407"]},{"raw_affiliation_string":"Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA","institution_ids":["https://openalex.org/I4388891891","https://openalex.org/I867280407"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5090203652"],"corresponding_institution_ids":["https://openalex.org/I4210096815","https://openalex.org/I4388891891","https://openalex.org/I867280407"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.9126,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.73335556,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"18","issue":"1","first_page":"448","last_page":"448"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.7021999955177307,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.7021999955177307,"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/T11668","display_name":"interferon and immune responses","score":0.04050000011920929,"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"}},{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.038100000470876694,"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":0.7636992931365967},{"id":"https://openalex.org/keywords/barcode","display_name":"Barcode","score":0.7386522889137268},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6274738311767578},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.577246367931366},{"id":"https://openalex.org/keywords/multiplexing","display_name":"Multiplexing","score":0.41015511751174927},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3881232738494873},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.18010300397872925},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11596599221229553}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7636992931365967},{"id":"https://openalex.org/C2776841711","wikidata":"https://www.wikidata.org/wiki/Q856","display_name":"Barcode","level":2,"score":0.7386522889137268},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6274738311767578},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.577246367931366},{"id":"https://openalex.org/C19275194","wikidata":"https://www.wikidata.org/wiki/Q222903","display_name":"Multiplexing","level":2,"score":0.41015511751174927},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3881232738494873},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.18010300397872925},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11596599221229553},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D007074","descriptor_name":"Immunoglobulin G","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007074","descriptor_name":"Immunoglobulin G","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007074","descriptor_name":"Immunoglobulin G","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":"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":"D017931","descriptor_name":"DNA Primers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017931","descriptor_name":"DNA Primers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-017-1853-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1853-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1853-z","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:29020925","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29020925","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:ark:/13030/qt5pz4g4w3","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:26c993d5cb694e45b75adc076995ae4a","is_oa":false,"landing_page_url":"https://doaj.org/article/26c993d5cb694e45b75adc076995ae4a","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 18, Iss 1, Pp 1-5 (2017)","raw_type":"article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt5pz4g4w3","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/5pz4g4w3","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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, vol 18, iss 1","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5637252","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5637252","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/s12859-017-1853-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1853-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1853-z","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/G1457999924","display_name":null,"funder_award_id":"4R01AI097403-05","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G1658833210","display_name":null,"funder_award_id":"HHSN272201200028C","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G2794496480","display_name":null,"funder_award_id":"HHSN272201200028C","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3280257","display_name":null,"funder_award_id":"R01AI097403","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G5162051383","display_name":null,"funder_award_id":"U19A1057229","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5276645557","display_name":null,"funder_award_id":"AI097403","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"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/W2761002607.pdf","grobid_xml":"https://content.openalex.org/works/W2761002607.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W869326979","https://openalex.org/W1547859938","https://openalex.org/W1570756084","https://openalex.org/W1883768105","https://openalex.org/W1978518799","https://openalex.org/W1984199376","https://openalex.org/W2013903972","https://openalex.org/W2042786738","https://openalex.org/W2051241958","https://openalex.org/W2087064593","https://openalex.org/W2097816699","https://openalex.org/W2105195133","https://openalex.org/W2105588743","https://openalex.org/W2109911015","https://openalex.org/W2119736800","https://openalex.org/W2136169373","https://openalex.org/W2140323624","https://openalex.org/W2151558930","https://openalex.org/W2172403535","https://openalex.org/W2175702062","https://openalex.org/W2310172832","https://openalex.org/W2460280360","https://openalex.org/W2592270809","https://openalex.org/W2761002607"],"related_works":["https://openalex.org/W2256570403","https://openalex.org/W2074156223","https://openalex.org/W2901653204","https://openalex.org/W2102526470","https://openalex.org/W4378447789","https://openalex.org/W2613659923","https://openalex.org/W3207557903","https://openalex.org/W2803056468","https://openalex.org/W1980504858","https://openalex.org/W4289655748"],"abstract_inverted_index":{"BACKGROUND:":[0],"Pre-processing":[1],"of":[2,96,139,156],"high-throughput":[3],"sequencing":[4,148,177],"data":[5,39,178],"for":[6,17,127,145,172],"immune":[7,146,175],"repertoire":[8,147,176],"profiling":[9],"is":[10,21,109,125,165,170],"essential":[11],"to":[12,102,112],"insure":[13],"high":[14],"quality":[15,53,56],"input":[16,101],"downstream":[18],"analysis.":[19],"VDJPipe":[20,46,78,124,153,164],"a":[22,34,80,90,141,166],"flexible,":[23],"high-performance":[24,167],"tool":[25,144,168],"that":[26,152,169],"can":[27],"perform":[28],"multiple":[29,84],"pre-processing":[30,143,173],"tasks":[31,43],"with":[32,93,137],"just":[33],"single":[35],"pass":[36],"over":[37],"the":[38,94,103,114,157],"files.":[40],"RESULTS:":[41],"Processing":[42],"provided":[44],"by":[45,133,161],"include":[47],"base":[48],"composition":[49],"statistics":[50,54],"calculation,":[51,55],"read":[52],"filtering,":[57,59,63],"homopolymer":[58],"length":[60],"and":[61,69,74],"nucleotide":[62],"paired-read":[64],"merging,":[65],"barcode":[66],"demultiplexing,":[67],"5'":[68],"3'":[70],"PCR":[71],"primer":[72],"matching,":[73],"duplicate":[75],"reads":[76],"collapsing.":[77],"utilizes":[79],"pipeline":[81],"approach":[82],"whereby":[83],"processing":[85],"steps":[86],"are":[87],"performed":[88],"in":[89,119],"sequential":[91],"workflow,":[92],"output":[95],"each":[97],"step":[98,105],"passed":[99],"as":[100],"next":[104],"automatically.":[106],"The":[107],"workflow":[108],"flexible":[110],"enough":[111],"handle":[113],"complex":[115],"barcoding":[116],"schemes":[117],"used":[118],"many":[120],"immunosequencing":[121],"experiments.":[122],"Because":[123],"designed":[126],"computational":[128],"efficiency,":[129],"we":[130],"evaluated":[131],"this":[132],"comparing":[134],"execution":[135],"times":[136],"those":[138],"pRESTO,":[140],"widely-used":[142],"data.":[149],"We":[150],"found":[151],"requires":[154],"<10%":[155],"run":[158],"time":[159],"required":[160],"pRESTO.":[162],"CONCLUSIONS:":[163],"optimized":[171],"large":[174],"sets.":[179]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
