{"id":"https://openalex.org/W1987545661","doi":"https://doi.org/10.1186/1471-2105-11-38","title":"SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read","display_name":"SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read","publication_year":2010,"publication_date":"2010-01-20","ids":{"openalex":"https://openalex.org/W1987545661","doi":"https://doi.org/10.1186/1471-2105-11-38","mag":"1987545661","pmid":"https://pubmed.ncbi.nlm.nih.gov/20089148"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-38","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-38","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-38","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/10.1186/1471-2105-11-38","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011828654","display_name":"Juan Falgueras","orcid":"https://orcid.org/0000-0002-5007-5911"},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Juan Falgueras","raw_affiliation_strings":["Departamento de Lenguajes y Ciencias de la Computaci\u00f3n, Universidad de M\u00e1laga, M\u00e1laga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Lenguajes y Ciencias de la Computaci\u00f3n, Universidad de M\u00e1laga, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102052893","display_name":"Antonio J. Lara","orcid":null},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Antonio J Lara","raw_affiliation_strings":["Plataforma Andaluza de Bioinform\u00e1tica, Universidad de M\u00e1laga, 29071, M\u00e1laga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Plataforma Andaluza de Bioinform\u00e1tica, Universidad de M\u00e1laga, 29071, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004035700","display_name":"No\u00e9 Fern\u00e1ndez\u2010Pozo","orcid":"https://orcid.org/0000-0002-6489-5566"},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"No\u00e9 Fern\u00e1ndez-Pozo","raw_affiliation_strings":["Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica, Universidad de M\u00e1laga, 29071, M\u00e1laga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica, Universidad de M\u00e1laga, 29071, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026821618","display_name":"Francisco R. Cant\u00f3n","orcid":"https://orcid.org/0000-0001-6917-8630"},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Francisco R Cant\u00f3n","raw_affiliation_strings":["Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica, Universidad de M\u00e1laga, 29071, M\u00e1laga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica, Universidad de M\u00e1laga, 29071, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047635872","display_name":"Guillermo P\u00e9rez-Trabado","orcid":"https://orcid.org/0000-0001-7567-9677"},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Guillermo P\u00e9rez-Trabado","raw_affiliation_strings":["Departamento de Arquitectura de Computadores, Universidad de M\u00e1laga, M\u00e1laga, Spain","Plataforma Andaluza de Bioinform\u00e1tica, Universidad de M\u00e1laga, 29071, M\u00e1laga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Arquitectura de Computadores, Universidad de M\u00e1laga, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I82767444"]},{"raw_affiliation_string":"Plataforma Andaluza de Bioinform\u00e1tica, Universidad de M\u00e1laga, 29071, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I82767444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056017872","display_name":"M. Gonzalo Claros","orcid":"https://orcid.org/0000-0002-0112-3550"},"institutions":[{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"M Gonzalo Claros","raw_affiliation_strings":["Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica, Universidad de M\u00e1laga, 29071, M\u00e1laga, Spain","Plataforma Andaluza de Bioinform\u00e1tica, Universidad de M\u00e1laga, 29071, M\u00e1laga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departamento de Biolog\u00eda Molecular y Bioqu\u00edmica, Universidad de M\u00e1laga, 29071, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I82767444"]},{"raw_affiliation_string":"Plataforma Andaluza de Bioinform\u00e1tica, Universidad de M\u00e1laga, 29071, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I82767444"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5056017872"],"corresponding_institution_ids":["https://openalex.org/I82767444"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":7.3428,"has_fulltext":true,"cited_by_count":198,"citation_normalized_percentile":{"value":0.98103128,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"11","issue":"1","first_page":"38","last_page":"38"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8233000040054321,"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":0.8233000040054321,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.03519999980926514,"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":0.019899999722838402,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7025623321533203},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6958047151565552},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5398278832435608},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.4676850438117981},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.4672520160675049},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.45533695816993713},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4492340683937073},{"id":"https://openalex.org/keywords/hybrid-genome-assembly","display_name":"Hybrid genome assembly","score":0.4481557309627533},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.43720579147338867},{"id":"https://openalex.org/keywords/pyrosequencing","display_name":"Pyrosequencing","score":0.42611706256866455},{"id":"https://openalex.org/keywords/shotgun-sequencing","display_name":"Shotgun sequencing","score":0.3320544362068176},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3258931636810303},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.258310467004776},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.2340030074119568},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19612911343574524},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.16114690899848938},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10725605487823486}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7025623321533203},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6958047151565552},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5398278832435608},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.4676850438117981},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.4672520160675049},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.45533695816993713},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4492340683937073},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.4481557309627533},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.43720579147338867},{"id":"https://openalex.org/C125009961","wikidata":"https://www.wikidata.org/wiki/Q2342248","display_name":"Pyrosequencing","level":3,"score":0.42611706256866455},{"id":"https://openalex.org/C101985253","wikidata":"https://www.wikidata.org/wiki/Q1073526","display_name":"Shotgun sequencing","level":4,"score":0.3320544362068176},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3258931636810303},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.258310467004776},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.2340030074119568},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19612911343574524},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.16114690899848938},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10725605487823486},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"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/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0}],"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":"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":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-11-38","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-38","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-38","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:20089148","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20089148","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:digital.csic.es:10261/343021","is_oa":true,"landing_page_url":"http://hdl.handle.net/10261/343021","pdf_url":null,"source":{"id":"https://openalex.org/S4306400616","display_name":"DIGITAL.CSIC (Spanish National Research Council (CSIC))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I134820265","host_organization_name":"Consejo Superior de Investigaciones Cient\u00edficas","host_organization_lineage":["https://openalex.org/I134820265"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"http://purl.org/coar/resource_type/c_6501"},{"id":"pmh:oai:doaj.org/article:59b6a5340bf0401c8e9d5103562fcc91","is_oa":false,"landing_page_url":"https://doaj.org/article/59b6a5340bf0401c8e9d5103562fcc91","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 11, Iss 1, p 38 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2832897","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2832897","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:10.1186/1471-2105-11-38","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-38","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-38","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":0.4699999988079071,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G1320307708","display_name":null,"funder_award_id":"BIO2009-07490","funder_id":"https://openalex.org/F4320326754","funder_display_name":"Junta de Andaluc\u00eda"},{"id":"https://openalex.org/G7825495982","display_name":null,"funder_award_id":"PLE2009","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G862819838","display_name":null,"funder_award_id":"BIO-114","funder_id":"https://openalex.org/F4320326754","funder_display_name":"Junta de Andaluc\u00eda"},{"id":"https://openalex.org/G863065016","display_name":null,"funder_award_id":"BIO2009-07490","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320326754","display_name":"Junta de Andaluc\u00eda","ror":"https://ror.org/01jem9c82"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1987545661.pdf","grobid_xml":"https://content.openalex.org/works/W1987545661.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W114797723","https://openalex.org/W1839674003","https://openalex.org/W1966585515","https://openalex.org/W1985726486","https://openalex.org/W1992685092","https://openalex.org/W2024312710","https://openalex.org/W2030311040","https://openalex.org/W2073497058","https://openalex.org/W2117490274","https://openalex.org/W2118867594","https://openalex.org/W2119923823","https://openalex.org/W2121016876","https://openalex.org/W2124943423","https://openalex.org/W2140770632","https://openalex.org/W2147772097","https://openalex.org/W2149585737","https://openalex.org/W2153211479","https://openalex.org/W2164124971"],"related_works":["https://openalex.org/W2008090296","https://openalex.org/W2213265806","https://openalex.org/W2166654698","https://openalex.org/W2440089543","https://openalex.org/W2165847428","https://openalex.org/W2043714862","https://openalex.org/W2166973401","https://openalex.org/W2047803783","https://openalex.org/W2157460239","https://openalex.org/W2147623421"],"abstract_inverted_index":{"BACKGROUND:":[0],"High-throughput":[1],"automated":[2],"sequencing":[3,11,205],"has":[4,43],"enabled":[5],"an":[6,141,183],"exponential":[7],"growth":[8],"rate":[9],"of":[10,31,86,147,150,182],"data.":[12],"This":[13],"requires":[14],"increasing":[15],"sequence":[16,66,96,151,185,196],"quality":[17],"and":[18,36,50,58,76,79,89,129,132,160,178,201],"reliability":[19],"in":[20,95],"order":[21],"to":[22,64,68,80,100,136,168,179],"avoid":[23],"database":[24],"contamination":[25],"with":[26,119,172],"artefactual":[27],"sequences.":[28],"The":[29,84,188],"arrival":[30],"pyrosequencing":[32,130],"enhances":[33],"this":[34],"problem":[35],"necessitates":[37],"customisable":[38],"pre-processing":[39,146,176,181],"algorithms.":[40],"RESULTS:":[41],"SeqTrim":[42,104,139],"been":[44,62],"implemented":[45,108],"both":[46],"as":[47,51,109],"a":[48,52,162],"Web":[49,110],"standalone":[53,113],"command":[54],"line":[55],"application.":[56],"Already-published":[57],"newly-designed":[59],"algorithms":[60],"have":[61],"included":[63],"identify":[65],"inserts,":[67],"remove":[69],"low":[70,74],"quality,":[71],"vector,":[72],"adaptor,":[73],"complexity":[75],"contaminant":[77],"sequences,":[78],"detect":[81],"chimeric":[82],"reads.":[83],"availability":[85],"several":[87],"input":[88],"output":[90],"formats":[91],"allows":[92,166],"its":[93,101],"inclusion":[94],"processing":[97],"workflows.":[98],"Due":[99],"specific":[102],"algorithms,":[103],"outperforms":[105],"other":[106],"pre-processors":[107,200],"services":[111],"or":[112,206],"applications.":[114],"It":[115,156],"performs":[116],"equally":[117],"well":[118],"sequences":[120,173],"from":[121],"EST":[122],"libraries,":[123,125],"SSH":[124],"genomic":[126],"DNA":[127],"libraries":[128],"reads":[131],"does":[133],"not":[134],"lead":[135],"over-trimming.":[137],"CONCLUSIONS:":[138],"is":[140,157],"efficient":[142],"pipeline":[143,190],"designed":[144],"for":[145],"any":[148],"type":[149],"read,":[152],"including":[153],"next-generation":[154],"sequencing.":[155],"easily":[158],"configurable":[159],"provides":[161],"friendly":[163],"interface":[164],"that":[165],"users":[167],"know":[169],"what":[170],"happened":[171],"at":[174],"every":[175],"stage,":[177],"verify":[180],"individual":[184],"if":[186],"desired.":[187],"recommended":[189],"reveals":[191],"more":[192,204],"information":[193],"about":[194],"each":[195],"than":[197],"previously":[198],"described":[199],"can":[202],"discard":[203],"experimental":[207],"artefacts.":[208]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":17},{"year":2015,"cited_by_count":12},{"year":2014,"cited_by_count":23},{"year":2013,"cited_by_count":20},{"year":2012,"cited_by_count":20}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
