{"@type": "dcat:Dataset", "accessLevel": "public", "bureauCode": ["005:18"], "contactPoint": {"fn": "Sim, Sheina B.", "hasEmail": "mailto:sheina.sim@usda.gov"}, "description": "<p dir=\"ltr\">The data in this repository is to provide the scripts used in the assembly of the <i>Bombus huntii </i>genome. It can be used to replicate the steps necessary to assemble the genome described in National Center for Biotechnology Information (NCBI) BioProject: <a href=\"https://www.ncbi.nlm.nih.gov/bioproject/858880\" rel=\"noreferrer\" target=\"_blank\">PRJNA858880</a>. This genome assembly workflow was performed on the United States Department of Agriculture (USDA) - SCINet/Mississippi State University High Performance Computing Cluster (HPC) Atlas and installed via Conda.</p><h2>Dependencies</h2><ul><li><a href=\"https://github.com/pezmaster31/bamtools\" target=\"_blank\">bamtools</a> v2.5.1</li><li><a href=\"https://github.com/madler/pigz\" target=\"_blank\">pigz</a> v2.6</li><li><a href=\"https://github.com/tseemann/any2fasta\" target=\"_blank\">any2fasta</a> v0.4.2</li><li><a href=\"https://docs.sylabs.io/guides/3.0/user-guide/installation.html\" rel=\"nofollow\" target=\"_blank\">Singularity</a> v3.8.3</li><li><a href=\"https://github.com/ncbi/fcs/wiki/FCS-adaptor\" target=\"_blank\">NCBI FCS adaptor</a></li><li><a href=\"https://github.com/sheinasim/HiFiAdapterFilt\" target=\"_blank\">HiFiAdapterFilt</a> v3.0.1</li><li><a href=\"https://github.com/chhylp123/hifiasm\" target=\"_blank\">HiFiASM</a> v0.19.3-r572</li><li><a href=\"https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/\" rel=\"nofollow\" target=\"_blank\">BBmap</a> v38.90</li><li><a href=\"https://github.com/refresh-bio/KMC\" target=\"_blank\">KMC</a> v3.2.1</li><li><a href=\"https://github.com/tbenavi1/genomescope2.0\" target=\"_blank\">GenomeScope2</a> v2.0</li><li><a href=\"https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html#downloadblastdata\" rel=\"nofollow\" target=\"_blank\">BLAST+</a> v2.0</li><li><a href=\"https://github.com/bbuchfink/diamond\" target=\"_blank\">diamond</a> v2.0.9</li><li><a href=\"https://github.com/lh3/minimap2\" target=\"_blank\">minimap2</a> v2.22-r1101</li><li><a href=\"https://github.com/blobtoolkit/blobtoolkit\" target=\"_blank\">blobtoolkit2</a> v4.1.5</li><li><a href=\"https://github.com/sheinasim/blobblurb\" target=\"_blank\">blobblurb</a> v1.2</li><li><a href=\"https://github.com/sheinasim/seqer\" target=\"_blank\">seqer</a> v1.2</li><li><a href=\"https://github.com/c-zhou/yahs\" rel=\"noreferrer\" target=\"_blank\">yahs</a> v1.1</li></ul><p dir=\"ltr\"><br></p>", "distribution": [{"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/46146393", "format": "sh", "mediaType": "text/x-shellscript", "title": "busco5.sh"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/46146396", "format": "sh", "mediaType": "text/x-shellscript", "title": "genomescope2.sh"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/46146399", "format": "sh", "mediaType": "text/x-shellscript", "title": "blob.sh"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/46146402", "format": "sh", "mediaType": "text/x-shellscript", "title": "hifiasm.sh"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/46146405", "format": "sh", "mediaType": "text/x-shellscript", "title": "hifiadapterfiltFCS.sh"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/46146408", "format": "sh", "mediaType": "text/x-shellscript", "title": "hic_yahs.sh"}], "identifier": "10.15482/USDA.ADC/25762431.v1", "keyword": ["Bombus hunti", "Hunt bumble bee", "genome assembly", "genome assembly protocol", "genome; chromosomes"], "license": "https://creativecommons.org/licenses/by-sa/4.0/", "modified": "2026-03-25", "programCode": ["005:040"], "publisher": {"@type": "org:Organization", "name": "Agricultural Research Service"}, "temporal": "2024-05-02/2024-05-02", "title": "Bombus huntii genome assembly scripts"}