{"id":"https://openalex.org/W3121244345","doi":"https://doi.org/10.1093/bib/bbaa429","title":"MITGARD: an automated pipeline for mitochondrial genome assembly in eukaryotic species using RNA-seq data","display_name":"MITGARD: an automated pipeline for mitochondrial genome assembly in eukaryotic species using RNA-seq data","publication_year":2020,"publication_date":"2020-12-23","ids":{"openalex":"https://openalex.org/W3121244345","doi":"https://doi.org/10.1093/bib/bbaa429","mag":"3121244345","pmid":"https://pubmed.ncbi.nlm.nih.gov/33515000"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa429","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa429","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083941266","display_name":"Pedro G. Nachtigall","orcid":"https://orcid.org/0000-0002-3196-0173"},"institutions":[{"id":"https://openalex.org/I2800423888","display_name":"Instituto Butantan","ror":"https://ror.org/01whwkf30","country_code":"BR","type":"facility","lineage":["https://openalex.org/I2800423888"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Pedro G Nachtigall","raw_affiliation_strings":["Laborat\u00f3rio Especial de Toxinologia Aplicada , CeTICS, Instituto Butantan, S\u00e3o Paulo, SP, 05503-900,","Laborat\u00f3rio Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, S\u00e3o Paulo, SP, 05503-900, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio Especial de Toxinologia Aplicada , CeTICS, Instituto Butantan, S\u00e3o Paulo, SP, 05503-900,","institution_ids":["https://openalex.org/I2800423888"]},{"raw_affiliation_string":"Laborat\u00f3rio Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, S\u00e3o Paulo, SP, 05503-900, Brazil","institution_ids":["https://openalex.org/I2800423888"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083058907","display_name":"Felipe G. Grazziotin","orcid":"https://orcid.org/0000-0001-9896-9722"},"institutions":[{"id":"https://openalex.org/I2800423888","display_name":"Instituto Butantan","ror":"https://ror.org/01whwkf30","country_code":"BR","type":"facility","lineage":["https://openalex.org/I2800423888"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Felipe G Grazziotin","raw_affiliation_strings":["Laborat\u00f3rio de Cole\u00e7\u00f5es Zool\u00f3gicas , Instituto Butantan, S\u00e3o Paulo, SP, 05503-900,","Laborat\u00f3rio de Cole\u00e7\u00f5es Zool\u00f3gicas, Instituto Butantan, S\u00e3o Paulo, SP, 05503-900, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio de Cole\u00e7\u00f5es Zool\u00f3gicas , Instituto Butantan, S\u00e3o Paulo, SP, 05503-900,","institution_ids":["https://openalex.org/I2800423888"]},{"raw_affiliation_string":"Laborat\u00f3rio de Cole\u00e7\u00f5es Zool\u00f3gicas, Instituto Butantan, S\u00e3o Paulo, SP, 05503-900, Brazil","institution_ids":["https://openalex.org/I2800423888"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036009540","display_name":"In\u00e1cio L.M. Junqueira-de-Azevedo","orcid":"https://orcid.org/0000-0003-4491-0180"},"institutions":[{"id":"https://openalex.org/I2800423888","display_name":"Instituto Butantan","ror":"https://ror.org/01whwkf30","country_code":"BR","type":"facility","lineage":["https://openalex.org/I2800423888"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"In\u00e1cio L M Junqueira-de-Azevedo","raw_affiliation_strings":["Laborat\u00f3rio Especial de Toxinologia Aplicada , CeTICS, Instituto Butantan, S\u00e3o Paulo, SP, 05503-900,","Laborat\u00f3rio Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, S\u00e3o Paulo, SP, 05503-900, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio Especial de Toxinologia Aplicada , CeTICS, Instituto Butantan, S\u00e3o Paulo, SP, 05503-900,","institution_ids":["https://openalex.org/I2800423888"]},{"raw_affiliation_string":"Laborat\u00f3rio Especial de Toxinologia Aplicada, CeTICS, Instituto Butantan, S\u00e3o Paulo, SP, 05503-900, Brazil","institution_ids":["https://openalex.org/I2800423888"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5083941266"],"corresponding_institution_ids":["https://openalex.org/I2800423888"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":null,"fwci":1.4228,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.81818875,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"22","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8766000270843506,"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":0.8766000270843506,"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/T12640","display_name":"Environmental DNA in Biodiversity Studies","score":0.031700000166893005,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10332","display_name":"Amphibian and Reptile Biology","score":0.021400000900030136,"subfield":{"id":"https://openalex.org/subfields/2306","display_name":"Global and Planetary Change"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7113803625106812},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.6997451782226562},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5639880299568176},{"id":"https://openalex.org/keywords/mitochondrial-dna","display_name":"Mitochondrial DNA","score":0.5252936482429504},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4967384934425354},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.4869290590286255},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39335405826568604},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3741203248500824},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.25809091329574585},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22406870126724243},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.16201388835906982},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.15330541133880615},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.06176513433456421}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7113803625106812},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6997451782226562},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5639880299568176},{"id":"https://openalex.org/C24586158","wikidata":"https://www.wikidata.org/wiki/Q27075","display_name":"Mitochondrial DNA","level":3,"score":0.5252936482429504},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4967384934425354},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.4869290590286255},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39335405826568604},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3741203248500824},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25809091329574585},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22406870126724243},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.16201388835906982},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.15330541133880615},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.06176513433456421}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D005057","descriptor_name":"Eukaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005057","descriptor_name":"Eukaryotic Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005057","descriptor_name":"Eukaryotic Cells","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":"D017837","descriptor_name":"Bothrops","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D017837","descriptor_name":"Bothrops","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D017837","descriptor_name":"Bothrops","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D017837","descriptor_name":"Bothrops","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017837","descriptor_name":"Bothrops","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017837","descriptor_name":"Bothrops","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054629","descriptor_name":"Genome, Mitochondrial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054629","descriptor_name":"Genome, Mitochondrial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054629","descriptor_name":"Genome, Mitochondrial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbaa429","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa429","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33515000","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33515000","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":"Briefings in bioinformatics","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.7300000190734863,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G4290916013","display_name":null,"funder_award_id":"2016/50,127-5","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G5547626716","display_name":null,"funder_award_id":"2013/074671","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G8140016130","display_name":null,"funder_award_id":"2018/26520-4","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"}],"funders":[{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W1495148515","https://openalex.org/W1920665686","https://openalex.org/W1968339870","https://openalex.org/W1972697151","https://openalex.org/W1975574050","https://openalex.org/W1986862590","https://openalex.org/W1991554311","https://openalex.org/W1995625340","https://openalex.org/W2004869583","https://openalex.org/W2011657487","https://openalex.org/W2014823215","https://openalex.org/W2025564038","https://openalex.org/W2061244247","https://openalex.org/W2069643667","https://openalex.org/W2074038593","https://openalex.org/W2102177537","https://openalex.org/W2107696927","https://openalex.org/W2110560983","https://openalex.org/W2116548284","https://openalex.org/W2118526609","https://openalex.org/W2124997220","https://openalex.org/W2130680472","https://openalex.org/W2135995399","https://openalex.org/W2137756176","https://openalex.org/W2141052558","https://openalex.org/W2154169047","https://openalex.org/W2157227447","https://openalex.org/W2163491783","https://openalex.org/W2164480958","https://openalex.org/W2166265186","https://openalex.org/W2170551349","https://openalex.org/W2170819005","https://openalex.org/W2259511390","https://openalex.org/W2289876562","https://openalex.org/W2466124354","https://openalex.org/W2481456127","https://openalex.org/W2520394767","https://openalex.org/W2535995078","https://openalex.org/W2561412234","https://openalex.org/W2563535234","https://openalex.org/W2572179555","https://openalex.org/W2598650907","https://openalex.org/W2604308930","https://openalex.org/W2758677856","https://openalex.org/W2769431800","https://openalex.org/W2789843538","https://openalex.org/W2795286036","https://openalex.org/W2795719805","https://openalex.org/W2800147381","https://openalex.org/W2803687985","https://openalex.org/W2892243332","https://openalex.org/W2894808609","https://openalex.org/W2902489750","https://openalex.org/W2924380563","https://openalex.org/W2950304818","https://openalex.org/W2950450943","https://openalex.org/W2950509696","https://openalex.org/W2970737708","https://openalex.org/W2972679514","https://openalex.org/W3135469167","https://openalex.org/W4206702770","https://openalex.org/W6642281654"],"related_works":["https://openalex.org/W2326369733","https://openalex.org/W4308441232","https://openalex.org/W2567787466","https://openalex.org/W2022430805","https://openalex.org/W2794386548","https://openalex.org/W4381279187","https://openalex.org/W1992950355","https://openalex.org/W2013063066","https://openalex.org/W2890379969","https://openalex.org/W1841715584"],"abstract_inverted_index":{"MOTIVATION:":[0],"Over":[1],"the":[2,5,58,79,110,120,127,137,155,171,178,182,193,218,246],"past":[3],"decade,":[4],"field":[6],"of":[7,26,34,123,129,148,157,184,195,215,251],"next-generation":[8],"sequencing":[9,141],"(NGS)":[10],"has":[11,28],"seen":[12],"dramatic":[13],"advances":[14],"in":[15,20,47,139,145,208],"methods":[16],"and":[17,104,143,189,248,253,263],"a":[18,23,96,106,146,202,212,235,259],"decrease":[19],"costs.":[21],"Consequently,":[22],"large":[24],"expansion":[25],"data":[27,62,84,207,255],"been":[29],"generated":[30],"by":[31],"NGS,":[32],"most":[33,48,196],"which":[35,209],"have":[36],"originated":[37],"from":[38,82,85,159,170,217],"RNA-sequencing":[39],"(RNA-seq)":[40],"experiments.":[41],"Because":[42],"mitochondrial":[43,51,80,91,121,197],"genes":[44],"are":[45,54,64],"expressed":[46],"eukaryotic":[49],"cells,":[50],"mRNA":[52],"sequences":[53],"usually":[55],"co-sequenced":[56],"within":[57],"target":[59,111,172],"transcriptome,":[60],"generating":[61],"that":[63,76,116,133,154,223],"commonly":[65],"underused":[66],"or":[67],"discarded.":[68],"Here,":[69],"we":[70,152,200,210],"present":[71],"MITGARD,":[72],"an":[73],"automated":[74],"pipeline":[75,89],"reliably":[77],"recovers":[78],"genome":[81],"RNA-seq":[83],"various":[86],"sources.":[87],"The":[88],"identifies":[90],"sequence":[92],"reads":[93],"based":[94],"on":[95,229,245],"phylogenetically":[97],"related":[98],"reference,":[99],"assembles":[100],"them":[101],"into":[102],"contigs,":[103],"extracts":[105],"complete":[107],"mtDNA":[108],"for":[109,227,242,256,266],"species.":[112],"RESULTS:":[113],"We":[114,131],"demonstrate":[115],"MITGARD":[117,134,224,232],"can":[118,135],"reconstruct":[119],"genomes":[122],"several":[124],"species":[125,161,173,185],"throughout":[126],"tree":[128,214],"life.":[130],"noticed":[132],"recover":[136,177],"mitogenomes":[138],"different":[140],"schemes":[142],"even":[144],"scenario":[147],"low-sequencing":[149],"depth.":[150],"Moreover,":[151],"showed":[153],"use":[156,183,228],"references":[158],"congeneric":[160],"diverging":[162,186],"up":[163],"to":[164,176,238,264],"30":[165,188],"million":[166],"years":[167],"ago":[168],"(MYA)":[169],"is":[174,225,233],"sufficient":[175],"entire":[179],"mitogenome,":[180],"whereas":[181],"between":[187],"60":[190],"MYA":[191],"allows":[192],"recovery":[194],"genes.":[198],"Additionally,":[199],"provide":[201],"case":[203],"study":[204],"with":[205],"original":[206],"estimate":[211],"phylogenetic":[213,247],"snakes":[216],"genus":[219],"Bothrops,":[220],"further":[221],"demonstrating":[222],"suitable":[226],"biodiversity":[230],"projects.":[231],"then":[234],"valuable":[236],"tool":[237],"obtain":[239],"high-quality":[240],"information":[241],"studies":[243],"focusing":[244],"evolutionary":[249],"aspects":[250],"eukaryotes":[252],"provides":[254],"easily":[257],"identifying":[258],"sample":[260],"using":[261,268],"barcoding,":[262],"check":[265],"cross-contamination":[267],"third-party":[269],"tools.":[270]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":8}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
