Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40238183", "kind": "science-record", "revision": 2, "content_hash": "sha256:c5357a9d335de1e9fc84365623ff8b09207491d619ab671e51f7f4080d9d0441", "created_at": "2026-11-01T20:30:24Z", "updated_at": "2026-11-01T21:35:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly.", "doi": "10.1093/bioinformatics/btaf175", "pmid": "40238183", "authors": ["Lia Obinu", "Timothy Booth", "Heleen De Weerd", "Urmi Trivedi", "Andrea Porceddu"], "journal": "Bioinformatics (Oxford, England)", "year": 2025, "abstract": "MOTIVATION: De novo assembly creates reference genomes that underpin many modern biodiversity and conservation studies. Large numbers of new genomes are being assembled by labs around the world. To avoid duplication of efforts and variable data quality, we desire a best-practice assembly process, implemented as an automated portable workflow.\nRESULTS: Here, we present Colora, a Snakemake workflow that produces chromosome-scale de novo primary or phased genome assemblies complete with organelles using Pacific Biosciences HiFi, Hi-C, and optionally Oxford Nanopore Technologies reads as input. Colora is a user-friendly, versatile, and reproducible pipeline that is ready to use by researchers looking for an automated way to obtain high-quality de novo genome assemblies.\nAVAILABILITY AND IMPLEMENTATION: The source code of Colora is available on GitHub (https://github.com/LiaOb21/colora) and has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576. Colora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora).", "claims": [{"id": "claim-method", "statement": "The k-mers are counted with KMC (Deorowicz et al. 2013, 2015, Kokot et al. 2017) from the PacBio HiFi reads, and the k-mer spectrum is plotted with GenomeScope2 (Rhyker Ranallo-Benavidez et al. 2020).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40238183", "locator": "sections[4] \"2.2 K-mers analysis, organelles, and genome assembly\" paragraph 2", "quote": "The k-mers are counted with KMC (Deorowicz et al. 2013, 2015, Kokot et al. 2017) from the PacBio HiFi reads, and the k-mer spectrum is plotted with GenomeScope2 (Rhyker Ranallo-Benavidez et al. 2020)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Project name: Colora\nProject home page: https://github.com/LiaOb21/colora\nOperating system(s): Linux\nProgramming language: Python, Bash, Perl, Awk\nOther requirements: Miniconda, Snakemake\nLicense: MIT\nColora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora) and the code has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576.\nThe public raw data used to test the workflow are available from the NCBI SRA database for R. irregularis (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=32643414) and M. domestica (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=26566345) and from the NGDC for A. thaliana (https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA005809).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40238183", "locator": "sections[25] \"Data availability\" paragraphs 1-9", "quote": "Project name: Colora\nProject home page: https://github.com/LiaOb21/colora\nOperating system(s): Linux\nProgramming language: Python, Bash, Perl, Awk\nOther requirements: Miniconda, Snakemake\nLicense: MIT\nColora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora) and the code has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576.\nThe public raw data used to test the workflow are available from the NCBI SRA database for R. irregularis (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=32643414) and M. domestica (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=26566345) and from the NGDC for A. thaliana (https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA005809)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40238183"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_unresolved", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PRJNA1013711"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PRJNA1013711"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_unresolved"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40238183", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1093/bioinformatics/btaf175", "sha256": "sha256:1bb28e164477ec4bbece57141b8231cfafee59958a9194a18df2dadf6723a830", "bytes": 30817, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1093/bioinformatics/btaf175", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12065627", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PRJNA1013711", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA1013711", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA1013711", "version": null, "note": "Project name: Colora\nProject home page: https://github.com/LiaOb21/colora\nOperating system(s): Linux\nProgramming language: Python, Bash, Perl, Awk\nOther requirements: Miniconda, Snakemake\nLicense: MIT\nColora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora) and the code has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576.\nThe public raw data used to test the workflow are available from the NCBI SRA database for R. irregularis (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=32643414) and M. domestica (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=26566345) and from the NGDC for A. thaliana (https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA005809).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Project name: Colora\nProject home page: https://github.com/LiaOb21/colora\nOperating system(s): Linux\nProgramming language: Python, Bash, Perl, Awk\nOther requirements: Miniconda, Snakemake\nLicense: MIT\nColora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora) and the code has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576.\nThe public raw data used to test the workflow are available from the NCBI SRA database for R. irregularis (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=32643414) and M. domestica (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=26566345) and from the NGDC for A. thaliana (https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA005809).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T20:16:20Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PRJNA1075684", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA1075684", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA1075684", "version": null, "note": "Project name: Colora\nProject home page: https://github.com/LiaOb21/colora\nOperating system(s): Linux\nProgramming language: Python, Bash, Perl, Awk\nOther requirements: Miniconda, Snakemake\nLicense: MIT\nColora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora) and the code has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576.\nThe public raw data used to test the workflow are available from the NCBI SRA database for R. irregularis (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=32643414) and M. domestica (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=26566345) and from the NGDC for A. thaliana (https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA005809).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Project name: Colora\nProject home page: https://github.com/LiaOb21/colora\nOperating system(s): Linux\nProgramming language: Python, Bash, Perl, Awk\nOther requirements: Miniconda, Snakemake\nLicense: MIT\nColora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora) and the code has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576.\nThe public raw data used to test the workflow are available from the NCBI SRA database for R. irregularis (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=32643414) and M. domestica (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=26566345) and from the NGDC for A. thaliana (https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA005809).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T20:16:20Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PRJNA814760", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA814760", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA814760", "version": null, "note": "Project name: Colora\nProject home page: https://github.com/LiaOb21/colora\nOperating system(s): Linux\nProgramming language: Python, Bash, Perl, Awk\nOther requirements: Miniconda, Snakemake\nLicense: MIT\nColora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora) and the code has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576.\nThe public raw data used to test the workflow are available from the NCBI SRA database for R. irregularis (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=32643414) and M. domestica (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=26566345) and from the NGDC for A. thaliana (https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA005809).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Project name: Colora\nProject home page: https://github.com/LiaOb21/colora\nOperating system(s): Linux\nProgramming language: Python, Bash, Perl, Awk\nOther requirements: Miniconda, Snakemake\nLicense: MIT\nColora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora) and the code has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576.\nThe public raw data used to test the workflow are available from the NCBI SRA database for R. irregularis (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=32643414) and M. domestica (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=26566345) and from the NGDC for A. thaliana (https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA005809).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T20:16:20Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PRJNA922099", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA922099", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA922099", "version": null, "note": "Project name: Colora\nProject home page: https://github.com/LiaOb21/colora\nOperating system(s): Linux\nProgramming language: Python, Bash, Perl, Awk\nOther requirements: Miniconda, Snakemake\nLicense: MIT\nColora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora) and the code has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576.\nThe public raw data used to test the workflow are available from the NCBI SRA database for R. irregularis (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=32643414) and M. domestica (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=26566345) and from the NGDC for A. thaliana (https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA005809).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Project name: Colora\nProject home page: https://github.com/LiaOb21/colora\nOperating system(s): Linux\nProgramming language: Python, Bash, Perl, Awk\nOther requirements: Miniconda, Snakemake\nLicense: MIT\nColora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora) and the code has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576.\nThe public raw data used to test the workflow are available from the NCBI SRA database for R. irregularis (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=32643414) and M. domestica (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=26566345) and from the NGDC for A. thaliana (https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA005809).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T20:16:20Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PRJNA1013711 not downloaded", "asset:data:geo:PRJNA1013711 licence not read", "asset:data:geo:PRJNA1075684 not downloaded", "asset:data:geo:PRJNA1075684 licence not read", "asset:data:geo:PRJNA814760 not downloaded", "asset:data:geo:PRJNA814760 licence not read", "asset:data:geo:PRJNA922099 not downloaded", "asset:data:geo:PRJNA922099 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "KM"}}, {"id": "method-2", "family": null, "specific": null, "label": "k-mer analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The k-mers are counted with KMC (Deorowicz et al. 2013, 2015, Kokot et al. 2017) from the PacBio HiFi reads, and the k-mer spectrum is plotted with GenomeScope2 (Rhyker Ranallo-Benavidez et al. 2020)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["PRJNA922099", "PRJNA814760", "PRJNA1075684", "PRJNA1013711"], "resolved_accessions": [], "statements": ["Project name: Colora\nProject home page: https://github.com/LiaOb21/colora\nOperating system(s): Linux\nProgramming language: Python, Bash, Perl, Awk\nOther requirements: Miniconda, Snakemake\nLicense: MIT\nColora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora) and the code has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576.\nThe public raw data used to test the workflow are available from the NCBI SRA database for R. irregularis (https://www.ncbi.nlm.nih.gov/sra? LinkName=biosample_sra&from_uid=32643414) and M. domestica (https://www.ncbi.nlm.nih.gov/sra? 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