{"id":"https://openalex.org/W3117723450","doi":"https://doi.org/10.1093/bib/bbaa368","title":"Pyfastx: a robust Python package for fast random access to sequences from plain and gzipped FASTA/Q files","display_name":"Pyfastx: a robust Python package for fast random access to sequences from plain and gzipped FASTA/Q files","publication_year":2020,"publication_date":"2020-11-18","ids":{"openalex":"https://openalex.org/W3117723450","doi":"https://doi.org/10.1093/bib/bbaa368","mag":"3117723450","pmid":"https://pubmed.ncbi.nlm.nih.gov/33341884"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa368","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa368","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":"software-paper","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/A5110275547","display_name":"Lianming Du","orcid":"https://orcid.org/0000-0003-0646-0887"},"institutions":[{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lianming Du","raw_affiliation_strings":["Institute for Advanced Study, Chengdu University, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Advanced Study, Chengdu University, Chengdu, China","institution_ids":["https://openalex.org/I4210125143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100432490","display_name":"Qin Liu","orcid":"https://orcid.org/0000-0001-9964-580X"},"institutions":[{"id":"https://openalex.org/I4210131342","display_name":"Yibin University","ror":"https://ror.org/03w8m2977","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210131342"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qin Liu","raw_affiliation_strings":["College of Life Sciences and Food Engineering, Yibin University, Yibin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Sciences and Food Engineering, Yibin University, Yibin, China","institution_ids":["https://openalex.org/I4210131342"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059120947","display_name":"Zhenxin Fan","orcid":"https://orcid.org/0000-0003-0422-9497"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenxin Fan","raw_affiliation_strings":["Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081984422","display_name":"Jie Tang","orcid":"https://orcid.org/0000-0002-8973-5200"},"institutions":[{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Tang","raw_affiliation_strings":["Institute for Advanced Study, Chengdu University, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Advanced Study, Chengdu University, Chengdu, China","institution_ids":["https://openalex.org/I4210125143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020499334","display_name":"Xiuyue Zhang","orcid":"https://orcid.org/0000-0002-9681-2905"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiuyue Zhang","raw_affiliation_strings":["Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103005407","display_name":"Megan Price","orcid":"https://orcid.org/0000-0001-6335-3039"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Megan Price","raw_affiliation_strings":["Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083607763","display_name":"Bisong Yue","orcid":"https://orcid.org/0000-0001-6731-538X"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bisong Yue","raw_affiliation_strings":["Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074492756","display_name":"Kelei Zhao","orcid":"https://orcid.org/0000-0002-2515-065X"},"institutions":[{"id":"https://openalex.org/I4210125143","display_name":"Chengdu University","ror":"https://ror.org/034z67559","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210125143"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Kelei Zhao","raw_affiliation_strings":["Institute for Advanced Study, Chengdu University, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Advanced Study, Chengdu University, Chengdu, China","institution_ids":["https://openalex.org/I4210125143"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5074492756","https://openalex.org/A5083607763"],"corresponding_institution_ids":["https://openalex.org/I24185976","https://openalex.org/I4210125143"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":26,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"4","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":0.9998999834060669,"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":0.9998999834060669,"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":0.9962000250816345,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9914000034332275,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8307486772537231},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8256030082702637},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.49745944142341614},{"id":"https://openalex.org/keywords/random-access","display_name":"Random access","score":0.47428470849990845},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4176880419254303},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.3558136224746704},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.33030813932418823}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8307486772537231},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8256030082702637},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.49745944142341614},{"id":"https://openalex.org/C101722063","wikidata":"https://www.wikidata.org/wiki/Q218825","display_name":"Random access","level":2,"score":0.47428470849990845},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4176880419254303},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3558136224746704},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.33030813932418823},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbaa368","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa368","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:33341884","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33341884","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":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.4699999988079071}],"awards":[{"id":"https://openalex.org/G3130798174","display_name":null,"funder_award_id":"2018RCTJ","funder_id":"https://openalex.org/F4320334145","funder_display_name":"Sichuan Association for Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320334145","display_name":"Sichuan Association for Science and Technology","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W2015292449","https://openalex.org/W2108234281","https://openalex.org/W2114850508","https://openalex.org/W2117608012","https://openalex.org/W2134526812","https://openalex.org/W2150934173","https://openalex.org/W2241763745","https://openalex.org/W2308359027","https://openalex.org/W2399769480","https://openalex.org/W2461458082","https://openalex.org/W2529838505","https://openalex.org/W2952681371","https://openalex.org/W2983817879","https://openalex.org/W6690241230"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W4287027380","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W3193760048","https://openalex.org/W2207495067","https://openalex.org/W1906486629"],"abstract_inverted_index":{"FASTA":[0],"and":[1,39,157,213],"FASTQ":[2],"are":[3],"the":[4,14,26,32,48,62,66,88,92,140,149,214],"most":[5,73,113],"widely":[6],"used":[7,135],"biological":[8],"data":[9,21,36,118],"formats":[10,43],"that":[11,184],"have":[12,51,76],"become":[13],"de":[15],"facto":[16],"standard":[17],"to":[18,61,79,98,116,138,144,160,190,202],"exchange":[19],"sequence":[20,35],"between":[22],"bioinformatics":[23],"tools.":[24],"With":[25],"avalanche":[27],"of":[28,34,58,64,87,154,171,173,178],"next-generation":[29],"sequencing":[30],"data,":[31],"amount":[33],"being":[37],"deposited":[38],"accessed":[40],"in":[41,152],"FASTA/Q":[42,84,103,167,198],"is":[44,109,183,217],"increasing":[45],"dramatically.":[46],"However,":[47],"existing":[49,74],"tools":[50,75,93,137,182],"very":[52],"low":[53],"efficiency":[54],"at":[55,220],"random":[56,158],"retrieval":[57],"subsequences":[59,193],"due":[60],"requirement":[63],"loading":[65],"entire":[67],"index":[68,81,156],"into":[69],"memory.":[70,90],"In":[71,122],"addition,":[72],"no":[77],"capability":[78],"build":[80],"for":[82,119],"large":[83,166],"files":[85,104,168,199],"because":[86],"limited":[89],"Furthermore,":[91],"do":[94],"not":[95],"provide":[96],"support":[97],"randomly":[99,191],"accessing":[100],"sequences":[101],"from":[102,195,210],"compressed":[105,197],"by":[106,112],"gzip,":[107],"which":[108],"extensively":[110],"adopted":[111],"public":[114],"databases":[115],"compress":[117],"saving":[120],"storage.":[121],"this":[123],"study,":[124],"we":[125],"developed":[126],"pyfastx":[127,147,179],"as":[128],"a":[129],"versatile":[130],"Python":[131],"package":[132],"with":[133,165,169],"commonly":[134],"command-line":[136],"overcome":[139],"above":[141],"limitations.":[142],"Compared":[143],"other":[145,181],"tools,":[146],"yielded":[148],"highest":[150],"performance":[151],"terms":[153],"building":[155],"access":[159],"sequences,":[161],"particularly":[162],"when":[163],"dealing":[164],"hundreds":[170],"millions":[172],"sequences.":[174],"A":[175],"key":[176],"advantage":[177],"over":[180],"it":[185],"offers":[186],"an":[187],"efficient":[188],"way":[189],"extract":[192],"directly":[194],"gzip":[196],"without":[200],"needing":[201],"uncompress":[203],"beforehand.":[204],"Pyfastx":[205],"can":[206],"easily":[207],"be":[208],"installed":[209],"PyPI":[211],"(https://pypi.org/project/pyfastx)":[212],"source":[215],"code":[216],"freely":[218],"available":[219],"https://github.com/lmdu/pyfastx.":[221]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":6}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
