{"id":"https://openalex.org/W2132962963","doi":"https://doi.org/10.1186/1471-2105-14-s11-s3","title":"Efficient digest of high-throughput sequencing data in a reproducible report","display_name":"Efficient digest of high-throughput sequencing data in a reproducible report","publication_year":2013,"publication_date":"2013-09-01","ids":{"openalex":"https://openalex.org/W2132962963","doi":"https://doi.org/10.1186/1471-2105-14-s11-s3","mag":"2132962963","pmid":"https://pubmed.ncbi.nlm.nih.gov/24564231"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-14-s11-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s11-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-S11-S3","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/10.1186/1471-2105-14-S11-S3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100443000","display_name":"Zhe Zhang","orcid":"https://orcid.org/0000-0002-6748-3356"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhe Zhang","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064934412","display_name":"Jeremy Leipzig","orcid":"https://orcid.org/0000-0001-7224-9620"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy Leipzig","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043017979","display_name":"Ariella Sasson","orcid":"https://orcid.org/0000-0003-0749-507X"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ariella Sasson","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000628196","display_name":"Angela M Yu","orcid":"https://orcid.org/0000-0001-5404-594X"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Angela M Yu","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007279402","display_name":"Juan C. Per\u00edn","orcid":null},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Juan C Perin","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015750970","display_name":"Hongbo Xie","orcid":"https://orcid.org/0000-0003-2223-0029"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hongbo M Xie","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086151737","display_name":"Mahdi Sarmady","orcid":"https://orcid.org/0000-0001-6069-804X"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mahdi Sarmady","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054800561","display_name":"Patrick V. Warren","orcid":null},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patrick V Warren","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101817826","display_name":"Peter S. White","orcid":"https://orcid.org/0000-0003-0313-033X"},"institutions":[{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]},{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter S White","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA","Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, PA, USA","Division of Oncology, The Children's Hospital of Philadelphia, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, PA, USA","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, PA, USA","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Division of Oncology, The Children's Hospital of Philadelphia, PA, USA","institution_ids":["https://openalex.org/I1335321130"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5100443000"],"corresponding_institution_ids":["https://openalex.org/I1335321130"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5985,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.69636494,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"14","issue":"S11","first_page":"S3","last_page":"S3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8823999762535095,"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":0.8823999762535095,"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":0.031700000166893005,"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":0.01850000023841858,"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/throughput","display_name":"Throughput","score":0.694162130355835},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5682854652404785},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5450683832168579},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5253127217292786},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5014910697937012},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2795414626598358},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1919282078742981},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.16120010614395142},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08846968412399292},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08581426739692688}],"concepts":[{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.694162130355835},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5682854652404785},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5450683832168579},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5253127217292786},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5014910697937012},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2795414626598358},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1919282078742981},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.16120010614395142},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08846968412399292},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08581426739692688},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","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}],"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":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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:10.1186/1471-2105-14-s11-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s11-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-S11-S3","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:24564231","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24564231","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:europepmc.org:2839530","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3846741","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3846741","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3846741","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:10.1186/1471-2105-14-s11-s3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s11-s3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-14-S11-S3","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/G5652007140","display_name":null,"funder_award_id":"P30-HD026979","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6183440658","display_name":null,"funder_award_id":"HD026979","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6643891721","display_name":null,"funder_award_id":"P30-HD026979","funder_id":"https://openalex.org/F4320337611","funder_display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337611","display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","ror":"https://ror.org/04byxyr05"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2132962963.pdf","grobid_xml":"https://content.openalex.org/works/W2132962963.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1520411860","https://openalex.org/W2002134496","https://openalex.org/W2046137036","https://openalex.org/W2061596350","https://openalex.org/W2079386574","https://openalex.org/W2085315239","https://openalex.org/W2092988184","https://openalex.org/W2108234281","https://openalex.org/W2112113834","https://openalex.org/W2132352688","https://openalex.org/W2146128933","https://openalex.org/W2148181482","https://openalex.org/W2153805608","https://openalex.org/W2160443244","https://openalex.org/W2160697532","https://openalex.org/W2169279496","https://openalex.org/W2171777347","https://openalex.org/W2259938310","https://openalex.org/W2519244818","https://openalex.org/W2582743722","https://openalex.org/W2885727518"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W4391913857","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"BACKGROUND:":[0],"High-throughput":[1],"sequencing":[2,37,120,127,166],"(HTS)":[3],"technologies":[4],"are":[5,181],"spearheading":[6],"the":[7,16,68,102,134,145,169],"accelerated":[8],"development":[9],"of":[10,19,55,67,91,115,179],"biomedical":[11,189],"research.":[12],"Processing":[13],"and":[14,74,98,129,137,144,148,156,168,176,193,203],"summarizing":[15],"large":[17],"amount":[18],"data":[20,93,197],"generated":[21,163],"by":[22,164,198],"HTS":[23,92,116,196],"presents":[24],"a":[25,41,59,82,105,124,200],"non-trivial":[26],"challenge":[27],"to":[28,35,40,72,85,99,123,140,191],"bioinformatics.":[29],"A":[30],"commonly":[31],"adopted":[32],"standard":[33],"is":[34,58,71],"store":[36],"reads":[38],"aligned":[39],"reference":[42,125],"genome":[43],"in":[44,95,104],"SAM":[45],"(Sequence":[46],"Alignment/Map)":[47,51],"or":[48],"BAM":[49,96,161],"(Binary":[50],"files.":[52],"Quality":[53],"control":[54],"SAM/BAM":[56],"files":[57,162],"critical":[60],"checkpoint":[61],"before":[62],"downstream":[63],"analysis.":[64],"The":[65,108],"goal":[66],"current":[69],"project":[70],"facilitate":[73],"standardize":[75],"this":[76],"process.":[77],"RESULTS:":[78],"We":[79],"developed":[80],"bamchop,":[81],"robust":[83],"program":[84],"efficiently":[86],"summarize":[87],"key":[88],"statistical":[89,142],"metrics":[90],"stored":[94],"files,":[97],"visually":[100],"present":[101],"results":[103],"formatted":[106],"report.":[107],"report":[109],"documents":[110],"information":[111],"about":[112],"various":[113],"aspects":[114],"data,":[117],"such":[118],"as":[119],"quality,":[121],"mapping":[122],"genome,":[126],"coverage,":[128],"base":[130],"frequency.":[131],"Bamchop":[132,187],"uses":[133],"R":[135],"language":[136],"Bioconductor":[138],"packages":[139],"calculate":[141],"matrices":[143],"Sweave":[146],"utility":[147],"associated":[149],"LaTeX":[150],"markup":[151],"for":[152],"documentation.":[153],"Bamchop's":[154],"efficiency":[155],"robustness":[157],"were":[158],"tested":[159],"on":[160],"local":[165],"facilities":[167],"1000":[170],"Genomes":[171],"Project.":[172],"Source":[173],"code,":[174],"instruction":[175],"example":[177],"reports":[178],"bamchop":[180],"freely":[182],"available":[183],"from":[184],"https://github.com/CBMi-BiG/bamchop.":[185],"CONCLUSIONS:":[186],"enables":[188],"researchers":[190],"quickly":[192],"rigorously":[194],"evaluate":[195],"providing":[199],"convenient":[201],"synopsis":[202],"user-friendly":[204],"reports.":[205]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
