{"id":"https://openalex.org/W2138019459","doi":"https://doi.org/10.1186/1471-2105-15-s11-s10","title":"SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data","display_name":"SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data","publication_year":2014,"publication_date":"2014-10-21","ids":{"openalex":"https://openalex.org/W2138019459","doi":"https://doi.org/10.1186/1471-2105-15-s11-s10","mag":"2138019459","pmid":"https://pubmed.ncbi.nlm.nih.gov/25349885"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-s11-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s11-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S11-S10","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/10.1186/1471-2105-15-S11-S10","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027195327","display_name":"Yan Peng","orcid":"https://orcid.org/0000-0001-6086-0609"},"institutions":[{"id":"https://openalex.org/I44854399","display_name":"University of Southern Mississippi","ror":"https://ror.org/0270vfa57","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I44854399"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yan Peng","raw_affiliation_strings":["School of Computing, University of Southern Mississippi, Hattiesburg, MS, 39406, USA","School of Computing, University of Southern Mississippi, Hattiesburg, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, University of Southern Mississippi, Hattiesburg, MS, 39406, USA","institution_ids":["https://openalex.org/I44854399"]},{"raw_affiliation_string":"School of Computing, University of Southern Mississippi, Hattiesburg, USA","institution_ids":["https://openalex.org/I44854399"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035291496","display_name":"Andrew Maxwell","orcid":"https://orcid.org/0000-0002-6503-4661"},"institutions":[{"id":"https://openalex.org/I44854399","display_name":"University of Southern Mississippi","ror":"https://ror.org/0270vfa57","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I44854399"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew S Maxwell","raw_affiliation_strings":["School of Computing, University of Southern Mississippi, Hattiesburg, MS, 39406, USA","School of Computing, University of Southern Mississippi, Hattiesburg, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, University of Southern Mississippi, Hattiesburg, MS, 39406, USA","institution_ids":["https://openalex.org/I44854399"]},{"raw_affiliation_string":"School of Computing, University of Southern Mississippi, Hattiesburg, USA","institution_ids":["https://openalex.org/I44854399"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103851310","display_name":"Natalie D. Barker","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Natalie D Barker","raw_affiliation_strings":["Badger Technical Services, LLC, San Antonio, TX, 78216, USA","Badger Technical Services, LLC, San Antonio, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Badger Technical Services, LLC, San Antonio, TX, 78216, USA","institution_ids":[]},{"raw_affiliation_string":"Badger Technical Services, LLC, San Antonio, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047262254","display_name":"Jennifer G. Laird","orcid":null},"institutions":[{"id":"https://openalex.org/I4210088792","display_name":"United States Army","ror":"https://ror.org/00afsp483","country_code":"US","type":"government","lineage":["https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I4210088792"]},{"id":"https://openalex.org/I87303767","display_name":"U.S. Army Engineer Research and Development Center","ror":"https://ror.org/027mhn368","country_code":"US","type":"facility","lineage":["https://openalex.org/I1304082316","https://openalex.org/I1306490931","https://openalex.org/I1330347796","https://openalex.org/I87303767"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jennifer G Laird","raw_affiliation_strings":["Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, 39180, USA","Environmental Laboratory, U. S. Army Engineer Research and Development Center, Vicksburg, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, 39180, USA","institution_ids":["https://openalex.org/I4210088792","https://openalex.org/I87303767"]},{"raw_affiliation_string":"Environmental Laboratory, U. S. Army Engineer Research and Development Center, Vicksburg, USA","institution_ids":["https://openalex.org/I87303767"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084241377","display_name":"Alan R. Kennedy","orcid":"https://orcid.org/0000-0003-2319-3725"},"institutions":[{"id":"https://openalex.org/I4210088792","display_name":"United States Army","ror":"https://ror.org/00afsp483","country_code":"US","type":"government","lineage":["https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I4210088792"]},{"id":"https://openalex.org/I87303767","display_name":"U.S. Army Engineer Research and Development Center","ror":"https://ror.org/027mhn368","country_code":"US","type":"facility","lineage":["https://openalex.org/I1304082316","https://openalex.org/I1306490931","https://openalex.org/I1330347796","https://openalex.org/I87303767"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alan J Kennedy","raw_affiliation_strings":["Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, 39180, USA","Environmental Laboratory, U. S. Army Engineer Research and Development Center, Vicksburg, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, 39180, USA","institution_ids":["https://openalex.org/I4210088792","https://openalex.org/I87303767"]},{"raw_affiliation_string":"Environmental Laboratory, U. S. Army Engineer Research and Development Center, Vicksburg, USA","institution_ids":["https://openalex.org/I87303767"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100332786","display_name":"Nan Wang","orcid":"https://orcid.org/0000-0003-1743-3585"},"institutions":[{"id":"https://openalex.org/I44854399","display_name":"University of Southern Mississippi","ror":"https://ror.org/0270vfa57","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I44854399"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nan Wang","raw_affiliation_strings":["School of Computing, University of Southern Mississippi, Hattiesburg, MS, 39406, USA","School of Computing, University of Southern Mississippi, Hattiesburg, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, University of Southern Mississippi, Hattiesburg, MS, 39406, USA","institution_ids":["https://openalex.org/I44854399"]},{"raw_affiliation_string":"School of Computing, University of Southern Mississippi, Hattiesburg, USA","institution_ids":["https://openalex.org/I44854399"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100603445","display_name":"Chaoyang Zhang","orcid":"https://orcid.org/0000-0002-1221-0406"},"institutions":[{"id":"https://openalex.org/I44854399","display_name":"University of Southern Mississippi","ror":"https://ror.org/0270vfa57","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I44854399"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chaoyang Zhang","raw_affiliation_strings":["School of Computing, University of Southern Mississippi, Hattiesburg, MS, 39406, USA","School of Computing, University of Southern Mississippi, Hattiesburg, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, University of Southern Mississippi, Hattiesburg, MS, 39406, USA","institution_ids":["https://openalex.org/I44854399"]},{"raw_affiliation_string":"School of Computing, University of Southern Mississippi, Hattiesburg, USA","institution_ids":["https://openalex.org/I44854399"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019029265","display_name":"Ping Gong","orcid":"https://orcid.org/0000-0001-9910-7948"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Ping Gong","raw_affiliation_strings":["Badger Technical Services, LLC, San Antonio, TX, 78216, USA","Badger Technical Services, LLC, San Antonio, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Badger Technical Services, LLC, San Antonio, TX, 78216, USA","institution_ids":[]},{"raw_affiliation_string":"Badger Technical Services, LLC, San Antonio, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5019029265","https://openalex.org/A5100603445"],"corresponding_institution_ids":["https://openalex.org/I44854399"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.5198,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.65018282,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"15","issue":"S11","first_page":"S10","last_page":"S10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8774999976158142,"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":0.8774999976158142,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.041999999433755875,"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/T11482","display_name":"RNA modifications and cancer","score":0.008799999952316284,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6910813450813293},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6443188786506653},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5326191186904907},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4901169240474701},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.46862226724624634},{"id":"https://openalex.org/keywords/redundancy","display_name":"Redundancy (engineering)","score":0.45273274183273315},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.45258980989456177},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.4488421678543091},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.4445193409919739},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.41797545552253723},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3769003748893738},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3630622625350952},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2548418641090393},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22583135962486267},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18046405911445618},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11530718207359314},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10020601749420166}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6910813450813293},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6443188786506653},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5326191186904907},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4901169240474701},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46862226724624634},{"id":"https://openalex.org/C152124472","wikidata":"https://www.wikidata.org/wiki/Q1204361","display_name":"Redundancy (engineering)","level":2,"score":0.45273274183273315},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.45258980989456177},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.4488421678543091},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.4445193409919739},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.41797545552253723},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3769003748893738},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3630622625350952},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2548418641090393},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22583135962486267},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18046405911445618},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11530718207359314},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10020601749420166},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0}],"mesh":[{"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":"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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-15-s11-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s11-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S11-S10","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:25349885","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25349885","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:aquila.usm.edu:fac_pubs-19245","is_oa":false,"landing_page_url":"https://aquila.usm.edu/fac_pubs/17932","pdf_url":null,"source":{"id":"https://openalex.org/S4306402529","display_name":"Aquila Digital Community (University of Southern Mississippi)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I44854399","host_organization_name":"University of Southern Mississippi","host_organization_lineage":["https://openalex.org/I44854399"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:4251038","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4251038","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:10.1186/1471-2105-15-s11-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s11-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S11-S10","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":0.6399999856948853,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G116562658","display_name":null,"funder_award_id":"EPS 0903787","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6805318589","display_name":"Modeling and Simulation of Complex Systems","funder_award_id":"0903787","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2138019459.pdf","grobid_xml":"https://content.openalex.org/works/W2138019459.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1220385903","https://openalex.org/W1921457844","https://openalex.org/W1971899779","https://openalex.org/W1979946545","https://openalex.org/W1981509058","https://openalex.org/W2039486775","https://openalex.org/W2062235227","https://openalex.org/W2065817684","https://openalex.org/W2078562176","https://openalex.org/W2096173343","https://openalex.org/W2096791516","https://openalex.org/W2102532874","https://openalex.org/W2103441770","https://openalex.org/W2103903744","https://openalex.org/W2108234281","https://openalex.org/W2109636763","https://openalex.org/W2123402634","https://openalex.org/W2128945836","https://openalex.org/W2134153749","https://openalex.org/W2139993758","https://openalex.org/W2154397429","https://openalex.org/W2170999689","https://openalex.org/W4247053599"],"related_works":["https://openalex.org/W4210830088","https://openalex.org/W2767590279","https://openalex.org/W2584868213","https://openalex.org/W2079322808","https://openalex.org/W2216477337","https://openalex.org/W2794893153","https://openalex.org/W2721624558","https://openalex.org/W3011183076","https://openalex.org/W2166654698","https://openalex.org/W2949865853"],"abstract_inverted_index":{"BACKGROUND:":[0],"While":[1],"next-generation":[2],"sequencing":[3,209,214,251,309],"(NGS)":[4],"technologies":[5],"are":[6,182,216],"rapidly":[7],"advancing,":[8],"an":[9,30,106],"area":[10],"that":[11,287],"lags":[12],"behind":[13],"is":[14,206,281],"the":[15,40,70,73,99,132,136,145,154,163,168,186,213,229,233,248,255],"development":[16],"of":[17,25,43,89,94,111,123,141,144,235,250,298],"efficient":[18],"and":[19,46,79,86,115,120,128,139,152,194,245,265,284,310],"user-friendly":[20],"tools":[21],"for":[22,76,240,254],"preliminary":[23],"analysis":[24],"massive":[26],"NGS":[27,90,107,146,159,170,272],"data.":[28,91],"As":[29],"effort":[31],"to":[32,36,47,81,161,184,294],"fill":[33],"this":[34],"gap":[35],"keep":[37],"up":[38],"with":[39,126],"fast":[41],"pace":[42],"technological":[44],"advancement":[45],"accelerate":[48],"data-to-results":[49],"turnaround,":[50],"we":[51],"developed":[52],"a":[53,83,121,149,197,218,236,262,282,291,295],"novel":[54],"software":[55],"package":[56],"named":[57],"SeqAssist":[58,64,175,179,260,280],"(\"Sequencing":[59],"Assistant\"":[60],"or":[61,176,204,221,242,305],"SA).":[62],"RESULTS:":[63],"takes":[65],"NGS-generated":[66],"FASTQ":[67],"files":[68,181],"as":[69,290],"input,":[71],"employs":[72],"BWA-MEM":[74],"aligner":[75],"sequence":[77],"alignment,":[78],"aims":[80],"provide":[82],"quick":[84],"overview":[85],"basic":[87,103],"statistics":[88,104,226],"It":[92],"consists":[93],"three":[95],"separate":[96],"workflows:":[97],"(1)":[98],"SA_RunStats":[100],"workflow":[101,134,156],"generates":[102],"about":[105],"dataset,":[108],"including":[109],"numbers":[110],"raw,":[112],"cleaned,":[113],"redundant":[114,212],"unique":[116,124],"reads,":[117,210],"redundancy":[118,164],"rate,":[119],"list":[122],"sequences":[125],"length":[127],"read":[129],"count;":[130],"(2)":[131],"SA_Run2Ref":[133],"estimates":[135],"breadth,":[137],"depth":[138],"evenness":[140],"genome-wide":[142],"coverage":[143],"dataset":[147,264],"at":[148],"nucleotide":[150],"resolution;":[151],"(3)":[153],"SA_Run2Run":[155],"compares":[157],"two":[158,169,223],"datasets":[160,273],"determine":[162],"(overlapping":[165],"rate)":[166],"between":[167,222],"runs.":[171,224],"Statistics":[172],"produced":[173],"by":[174,208],"derived":[177],"from":[178,275],"output":[180],"designed":[183],"inform":[185],"user:":[187],"whether,":[188],"what":[189],"percentage,":[190],"how":[191,195,211],"many":[192],"times":[193],"evenly":[196],"genomic":[198],"locus":[199],"(i.e.,":[200],"gene,":[201],"scaffold,":[202],"chromosome":[203],"genome)":[205],"covered":[207],"reads":[215],"in":[217,231,246],"single":[219],"run":[220],"These":[225],"can":[227,288],"guide":[228],"user":[230],"evaluating":[232],"quality":[234],"DNA":[237],"library":[238],"prepared":[239],"RNA-Seq":[241],"genome":[243,276,302,308],"(re-)sequencing":[244],"deciding":[247],"number":[249],"runs":[252],"required":[253],"library.":[256],"We":[257],"have":[258],"tested":[259],"using":[261,270],"synthetic":[263],"demonstrated":[266],"its":[267],"main":[268],"features":[269],"multiple":[271],"generated":[274],"re-sequencing":[277],"experiments.":[278,312],"CONCLUSIONS:":[279],"useful":[283],"informative":[285],"tool":[286],"serve":[289],"valuable":[292],"\"assistant\"":[293],"broad":[296],"range":[297],"investigators":[299],"who":[300],"conduct":[301],"re-sequencing,":[303],"RNA-Seq,":[304],"de":[306],"novo":[307],"assembly":[311]},"counts_by_year":[{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
