{"id":"https://openalex.org/W7130359026","doi":"https://doi.org/10.1093/bioinformatics/btag799","title":"rustybam : a composable toolkit for alignment analysis and visualization with SafFire","display_name":"rustybam : a composable toolkit for alignment analysis and visualization with SafFire","publication_year":2026,"publication_date":"2026-10-28","ids":{"openalex":"https://openalex.org/W7130359026","doi":"https://doi.org/10.1093/bioinformatics/btag799","pmid":"https://pubmed.ncbi.nlm.nih.gov/41756921","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/12934802"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag799","doi":"https://doi.org/10.1093/bioinformatics/btag799","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag799","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btag799/72556227/btag799.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btag799/72556227/btag799.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5160114470","display_name":"Cade Mirchandani","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cade Mirchandani","raw_affiliation_strings":["University of Utah Department of Human Genetics and Utah Center for Genetic Discovery, , Salt Lake City, UT 84112,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Utah Department of Human Genetics and Utah Center for Genetic Discovery, , Salt Lake City, UT 84112,","institution_ids":["https://openalex.org/I223532165"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012396646","display_name":"Mitchell Robert Vollger","orcid":"https://orcid.org/0000-0002-8651-1615","observed_orcids":["https://orcid.org/0000-0002-8651-1615"]},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mitchell R Vollger","raw_affiliation_strings":["University of Utah Department of Human Genetics and Utah Center for Genetic Discovery, , Salt Lake City, UT 84112,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Utah Department of Human Genetics and Utah Center for Genetic Discovery, , Salt Lake City, UT 84112,","institution_ids":["https://openalex.org/I223532165"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5012396646"],"corresponding_institution_ids":["https://openalex.org/I223532165"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":10.7639,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.98714451,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"42","issue":"11","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":0.9976000189781189,"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":0.9976000189781189,"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":0.0006000000284984708,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bam-alignment-file","display_name":"BAM alignment file","score":0.8960000276565552},{"id":"https://openalex.org/keywords/scaffolding","display_name":"scaffolding","score":0.8709999918937683},{"id":"https://openalex.org/keywords/rust-programming-language","display_name":"Rust","score":0.6710000038146973}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7289999723434448},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6050000190734863},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5949000120162964},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.5598999857902527},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.47760000824928284},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.37119999527931213},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.3569999933242798},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3490999937057495},{"id":"https://openalex.org/C2988343187","wikidata":"https://www.wikidata.org/wiki/Q1130645","display_name":"Open source software","level":3,"score":0.33889999985694885},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.33329999446868896},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3068999946117401},{"id":"https://openalex.org/C2983685735","wikidata":"https://www.wikidata.org/wiki/Q5227355","display_name":"Data source","level":2,"score":0.2513999938964844},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.25119999051094055}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btag799","doi":"https://doi.org/10.1093/bioinformatics/btag799","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag799","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btag799/72556227/btag799.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.64898/2026.02.16.706142","doi":"https://doi.org/10.64898/2026.02.16.706142","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.02.16.706142","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/02/17/2026.02.16.706142.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:41756921","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41756921","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,"listed_in":[],"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":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"},{"id":"pmid:42949121","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42949121","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,"listed_in":[],"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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12934802","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12934802/","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag799","doi":"https://doi.org/10.1093/bioinformatics/btag799","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag799","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btag799/72556227/btag799.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3156696751","display_name":null,"funder_award_id":"4R00GM155552","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G9000366682","display_name":null,"funder_award_id":"R00GM155552","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7130359026.pdf","grobid_xml":"https://content.openalex.org/works/W7130359026.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W2098380802","https://openalex.org/W2135415614","https://openalex.org/W2784788330","https://openalex.org/W2788194819","https://openalex.org/W2789843538","https://openalex.org/W4206249648","https://openalex.org/W4220999759","https://openalex.org/W4225379371","https://openalex.org/W4225696641","https://openalex.org/W4321112378","https://openalex.org/W4376133061","https://openalex.org/W4376133202","https://openalex.org/W4386113054","https://openalex.org/W4401386115","https://openalex.org/W4402816138","https://openalex.org/W4411088098"],"related_works":["https://openalex.org/W7204111070","https://openalex.org/W7099273128","https://openalex.org/W4254674227","https://openalex.org/W7100291317","https://openalex.org/W4368360816","https://openalex.org/W2147841875","https://openalex.org/W2107318366","https://openalex.org/W4289203213","https://openalex.org/W2111890322","https://openalex.org/W2101016096"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"present":[2],"rustybam,":[3],"a":[4,18],"Rust-based":[5],"command-line":[6],"toolkit":[7],"for":[8,21],"CIGAR-aware":[9],"manipulation":[10],"of":[11],"PAF":[12],"and":[13,16,43,65,86],"BAM":[14],"alignments,":[15],"SafFire,":[17],"browser-based":[19],"tool":[20],"interactive":[22],"genome":[23],"comparison":[24],"visualization":[25],"with":[26,73],"annotation":[27],"overlays.":[28],"rustybam's":[29],"composable":[30],"subcommands":[31],"provide":[32],"overlap":[33],"resolution,":[34],"coordinate":[35],"liftover,":[36],"alignment":[37],"splitting":[38],"at":[39,71,76,95],"structural":[40],"variants,":[41],"scaffolding,":[42],"identity":[44],"statistics.":[45],"AVAILABILITY":[46],"AND":[47],"IMPLEMENTATION:":[48],"Both":[49],"tools":[50],"are":[51,80,93],"open":[52],"source":[53,74],"under":[54],"the":[55],"MIT":[56],"license.":[57],"rustybam":[58,84],"is":[59,69],"available":[60,81,94],"via":[61],"Bioconda":[62],"(https://anaconda.org/bioconda/rustybam),":[63],"crates.io,":[64],"GitHub":[66],"(https://github.com/vollgerlab/rustybam).":[67],"SafFire":[68,87],"hosted":[70],"https://vollgerlab.com/SafFire/":[72],"code":[75],"https://github.com/vollgerlab/SafFire.":[77],"Archived":[78],"versions":[79],"on":[82],"Zenodo:":[83],"(https://doi.org/10.5281/zenodo.4654875)":[85],"(https://doi.org/10.5281/zenodo.5765964).":[88],"SUPPLEMENTARY":[89],"INFORMATION:":[90],"Supplementary":[91],"data":[92],"Bioinformatics":[96],"online.":[97]},"counts_by_year":[{"year":2026,"cited_by_count":7}],"updated_date":"2026-11-06T12:05:46.655746","created_date":"2026-02-19T00:00:00"}
