{"id":"https://openalex.org/W4409500816","doi":"https://doi.org/10.1093/bioinformatics/btaf175","title":"Colora: a Snakemake workflow for complete chromosome-scale <i>de novo</i> genome assembly","display_name":"Colora: a Snakemake workflow for complete chromosome-scale <i>de novo</i> genome assembly","publication_year":2025,"publication_date":"2025-04-14","ids":{"openalex":"https://openalex.org/W4409500816","doi":"https://doi.org/10.1093/bioinformatics/btaf175","pmid":"https://pubmed.ncbi.nlm.nih.gov/40238183"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf175","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf175","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf175/62940330/btaf175.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,"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"},"type":"article","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/btaf175/62940330/btaf175.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032064578","display_name":"Lia Obinu","orcid":"https://orcid.org/0000-0002-3208-323X"},"institutions":[{"id":"https://openalex.org/I159650629","display_name":"University of Sassari","ror":"https://ror.org/01bnjbv91","country_code":"IT","type":"education","lineage":["https://openalex.org/I159650629"]},{"id":"https://openalex.org/I4210137845","display_name":"Edinburgh Genomics","ror":"https://ror.org/02z3r7t23","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210137845"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB","IT"],"is_corresponding":false,"raw_author_name":"Lia Obinu","raw_affiliation_strings":["Department of Agricultural Sciences, University of Sassari , Viale Italia 39/a , Sassari, Sardinia, 07100,","Edinburgh Genomics, The University of Edinburgh , Ashworth Laboratories, The King's Buildings, Charlotte Auerbach Rd , Edinburgh, Scotland, EH9 3FL,","The University of Edinburgh Edinburgh Genomics, , Ashworth Laboratories, The King\u2019s Buildings, Charlotte Auerbach Road, Edinburgh, EH9 3FL, Scotland,","University of Sassari Department of Agricultural Sciences, , Viale Italia 39A, Sassari, 07100, Sardinia,"],"raw_orcid":"https://orcid.org/0000-0002-3208-323X","affiliations":[{"raw_affiliation_string":"Department of Agricultural Sciences, University of Sassari , Viale Italia 39/a , Sassari, Sardinia, 07100,","institution_ids":["https://openalex.org/I159650629"]},{"raw_affiliation_string":"Edinburgh Genomics, The University of Edinburgh , Ashworth Laboratories, The King's Buildings, Charlotte Auerbach Rd , Edinburgh, Scotland, EH9 3FL,","institution_ids":["https://openalex.org/I4210137845"]},{"raw_affiliation_string":"The University of Edinburgh Edinburgh Genomics, , Ashworth Laboratories, The King\u2019s Buildings, Charlotte Auerbach Road, Edinburgh, EH9 3FL, Scotland,","institution_ids":["https://openalex.org/I4210137845","https://openalex.org/I98677209"]},{"raw_affiliation_string":"University of Sassari Department of Agricultural Sciences, , Viale Italia 39A, Sassari, 07100, Sardinia,","institution_ids":["https://openalex.org/I159650629"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060841909","display_name":"Tim Booth","orcid":"https://orcid.org/0000-0003-2470-9519"},"institutions":[{"id":"https://openalex.org/I4210137845","display_name":"Edinburgh Genomics","ror":"https://ror.org/02z3r7t23","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210137845"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Timothy Booth","raw_affiliation_strings":["Edinburgh Genomics, The University of Edinburgh , Ashworth Laboratories, The King's Buildings, Charlotte Auerbach Rd , Edinburgh, Scotland, EH9 3FL,","The University of Edinburgh Edinburgh Genomics, , Ashworth Laboratories, The King\u2019s Buildings, Charlotte Auerbach Road, Edinburgh, EH9 3FL, Scotland,"],"raw_orcid":"https://orcid.org/0000-0003-2470-9519","affiliations":[{"raw_affiliation_string":"Edinburgh Genomics, The University of Edinburgh , Ashworth Laboratories, The King's Buildings, Charlotte Auerbach Rd , Edinburgh, Scotland, EH9 3FL,","institution_ids":["https://openalex.org/I4210137845"]},{"raw_affiliation_string":"The University of Edinburgh Edinburgh Genomics, , Ashworth Laboratories, The King\u2019s Buildings, Charlotte Auerbach Road, Edinburgh, EH9 3FL, Scotland,","institution_ids":["https://openalex.org/I4210137845","https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107019367","display_name":"Heleen De Weerd","orcid":"https://orcid.org/0009-0000-4969-1429"},"institutions":[{"id":"https://openalex.org/I4210137845","display_name":"Edinburgh Genomics","ror":"https://ror.org/02z3r7t23","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210137845"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Heleen De Weerd","raw_affiliation_strings":["Edinburgh Genomics, The University of Edinburgh , Ashworth Laboratories, The King's Buildings, Charlotte Auerbach Rd , Edinburgh, Scotland, EH9 3FL,","The University of Edinburgh Edinburgh Genomics, , Ashworth Laboratories, The King\u2019s Buildings, Charlotte Auerbach Road, Edinburgh, EH9 3FL, Scotland,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Edinburgh Genomics, The University of Edinburgh , Ashworth Laboratories, The King's Buildings, Charlotte Auerbach Rd , Edinburgh, Scotland, EH9 3FL,","institution_ids":["https://openalex.org/I4210137845"]},{"raw_affiliation_string":"The University of Edinburgh Edinburgh Genomics, , Ashworth Laboratories, The King\u2019s Buildings, Charlotte Auerbach Road, Edinburgh, EH9 3FL, Scotland,","institution_ids":["https://openalex.org/I4210137845","https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086687948","display_name":"Urmi Trivedi","orcid":"https://orcid.org/0000-0002-2056-4511"},"institutions":[{"id":"https://openalex.org/I4210137845","display_name":"Edinburgh Genomics","ror":"https://ror.org/02z3r7t23","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210137845"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Urmi Trivedi","raw_affiliation_strings":["Edinburgh Genomics, The University of Edinburgh , Ashworth Laboratories, The King's Buildings, Charlotte Auerbach Rd , Edinburgh, Scotland, EH9 3FL,","The University of Edinburgh Edinburgh Genomics, , Ashworth Laboratories, The King\u2019s Buildings, Charlotte Auerbach Road, Edinburgh, EH9 3FL, Scotland,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Edinburgh Genomics, The University of Edinburgh , Ashworth Laboratories, The King's Buildings, Charlotte Auerbach Rd , Edinburgh, Scotland, EH9 3FL,","institution_ids":["https://openalex.org/I4210137845"]},{"raw_affiliation_string":"The University of Edinburgh Edinburgh Genomics, , Ashworth Laboratories, The King\u2019s Buildings, Charlotte Auerbach Road, Edinburgh, EH9 3FL, Scotland,","institution_ids":["https://openalex.org/I4210137845","https://openalex.org/I98677209"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037881364","display_name":"Andrea Porceddu","orcid":"https://orcid.org/0000-0001-7126-9048"},"institutions":[{"id":"https://openalex.org/I159650629","display_name":"University of Sassari","ror":"https://ror.org/01bnjbv91","country_code":"IT","type":"education","lineage":["https://openalex.org/I159650629"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Andrea Porceddu","raw_affiliation_strings":["Department of Agricultural Sciences, University of Sassari , Viale Italia 39/a , Sassari, Sardinia, 07100,","University of Sassari Department of Agricultural Sciences, , Viale Italia 39A, Sassari, 07100, Sardinia,"],"raw_orcid":"https://orcid.org/0000-0001-7126-9048","affiliations":[{"raw_affiliation_string":"Department of Agricultural Sciences, University of Sassari , Viale Italia 39/a , Sassari, Sardinia, 07100,","institution_ids":["https://openalex.org/I159650629"]},{"raw_affiliation_string":"University of Sassari Department of Agricultural Sciences, , Viale Italia 39A, Sassari, 07100, Sardinia,","institution_ids":["https://openalex.org/I159650629"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.0923,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.75634944,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"41","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":0.9490000009536743,"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":0.9490000009536743,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.006800000090152025,"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"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.00419999985024333,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.889212965965271},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6469369530677795},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6246488690376282},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.5831732153892517},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5136946439743042},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3757581412792206},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21578195691108704},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.20736250281333923},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17522430419921875},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16097497940063477},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1257355511188507}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.889212965965271},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6469369530677795},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6246488690376282},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.5831732153892517},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5136946439743042},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3757581412792206},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21578195691108704},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.20736250281333923},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17522430419921875},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16097497940063477},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1257355511188507},{"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/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002875","descriptor_name":"Chromosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaf175","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf175","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf175/62940330/btaf175.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,"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":"pmid:40238183","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40238183","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12065627","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12065627","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:pure.ed.ac.uk:openaire/5eaf8c2d-2aa6-4020-a685-c14c6f2296cc","is_oa":true,"landing_page_url":"https://hdl.handle.net/20.500.11820/5eaf8c2d-2aa6-4020-a685-c14c6f2296cc","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"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":"Obinu, L, Booth, T, De Weerd, H, Trivedi, U & Porceddu, A 2025, 'Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly', Bioinformatics, vol. 41, no. 5, btaf175. https://doi.org/10.1093/bioinformatics/btaf175","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pure.ed.ac.uk:publications/5eaf8c2d-2aa6-4020-a685-c14c6f2296cc","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/5eaf8c2d-2aa6-4020-a685-c14c6f2296cc","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"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":"Obinu, L, Booth, T, De Weerd, H, Trivedi, U & Porceddu, A 2025, 'Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly', Bioinformatics, vol. 41, no. 5, btaf175. https://doi.org/10.1093/bioinformatics/btaf175","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf175","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf175","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf175/62940330/btaf175.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,"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":[{"score":0.7200000286102295,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320323343","display_name":"Universit\u00e0 degli Studi di Sassari","ror":"https://ror.org/01bnjbv91"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409500816.pdf","grobid_xml":"https://content.openalex.org/works/W4409500816.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1494075612","https://openalex.org/W2103441770","https://openalex.org/W2110417468","https://openalex.org/W2125266506","https://openalex.org/W2153325555","https://openalex.org/W2155628349","https://openalex.org/W2166583632","https://openalex.org/W2583363792","https://openalex.org/W2613409207","https://openalex.org/W2765745983","https://openalex.org/W2766504919","https://openalex.org/W2808352813","https://openalex.org/W2950698362","https://openalex.org/W2951278111","https://openalex.org/W2951912016","https://openalex.org/W2955134475","https://openalex.org/W3002362821","https://openalex.org/W3012094285","https://openalex.org/W3119817612","https://openalex.org/W3186309583","https://openalex.org/W3198332687","https://openalex.org/W3213656100","https://openalex.org/W3216110456","https://openalex.org/W4284884776","https://openalex.org/W4311663808","https://openalex.org/W4362458910","https://openalex.org/W4387955524","https://openalex.org/W4391262782","https://openalex.org/W4391753286","https://openalex.org/W4392155646","https://openalex.org/W4398202991","https://openalex.org/W4403881617","https://openalex.org/W4404426560","https://openalex.org/W6657337411","https://openalex.org/W6774850695","https://openalex.org/W6809428970"],"related_works":["https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W2794386548","https://openalex.org/W4381279187","https://openalex.org/W1992950355","https://openalex.org/W2013063066","https://openalex.org/W2890379969","https://openalex.org/W1841715584","https://openalex.org/W2766401759","https://openalex.org/W3134563641"],"abstract_inverted_index":{"MOTIVATION:":[0],"De":[1],"novo":[2,61,107],"assembly":[3,41],"creates":[4],"reference":[5],"genomes":[6,19],"that":[7,57,91],"underpin":[8],"many":[9],"modern":[10],"biodiversity":[11],"and":[12,33,75,88,123],"conservation":[13],"studies.":[14],"Large":[15],"numbers":[16],"of":[17,31,116],"new":[18],"are":[20],"being":[21],"assembled":[22],"by":[23,96],"labs":[24],"around":[25],"the":[26,137],"world.":[27],"To":[28],"avoid":[29],"duplication":[30],"efforts":[32],"variable":[34],"data":[35],"quality,":[36],"we":[37,51],"desire":[38],"a":[39,54,85],"best-practice":[40],"process,":[42],"implemented":[43],"as":[44,81],"an":[45,100],"automated":[46,101],"portable":[47],"workflow.":[48],"RESULTS:":[49],"Here,":[50],"present":[52],"Colora,":[53],"Snakemake":[55,138],"workflow":[56],"produces":[58],"chromosome-scale":[59],"de":[60,106],"primary":[62],"or":[63],"phased":[64],"genome":[65,108],"assemblies":[66],"complete":[67],"with":[68],"organelles":[69],"using":[70],"Pacific":[71],"Biosciences":[72],"HiFi,":[73],"Hi-C,":[74],"optionally":[76],"Oxford":[77],"Nanopore":[78],"Technologies":[79],"reads":[80],"input.":[82],"Colora":[83,117,132],"is":[84,92,118,133],"user-friendly,":[86],"versatile,":[87],"reproducible":[89],"pipeline":[90],"ready":[93],"to":[94,103],"use":[95],"researchers":[97],"looking":[98],"for":[99],"way":[102],"obtain":[104],"high-quality":[105],"assemblies.":[109],"AVAILABILITY":[110],"AND":[111],"IMPLEMENTATION:":[112],"The":[113],"source":[114],"code":[115],"available":[119,135],"on":[120],"GitHub":[121],"(https://github.com/LiaOb21/colora)":[122],"has":[124],"been":[125],"deposited":[126],"in":[127],"Zenodo":[128],"under":[129],"DOI":[130],"https://doi.org/10.5281/zenodo.13321576.":[131],"also":[134],"at":[136],"Workflow":[139],"Catalog":[140],"(https://snakemake.github.io/snakemake-workflow-catalog/?":[141],"usage=LiaOb21%2Fcolora).":[142]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-04-17T00:00:00"}
