Bombus huntii genome assembly scripts
The data in this repository is to provide the scripts used in the assembly of the Bombus huntii genome. It can be used to replicate the steps necessary to assemble the genome described in National Center for Biotechnology Information (NCBI) BioProject: PRJNA858880. 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.Dependenciesbamtools v2.5.1pigz v2.6any2fasta v0.4.2Singularity v3.8.3NCBI FCS adaptorHiFiAdapterFilt v3.0.1HiFiASM v0.19.3-r572BBmap v38.90KMC v3.2.1GenomeScope2 v2.0BLAST+ v2.0diamond v2.0.9minimap2 v2.22-r1101blobtoolkit2 v4.1.5blobblurb v1.2seqer v1.2yahs v1.1
Resources
6 resources available
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busco5.sh
SH -
genomescope2.sh
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blob.sh
SH -
hifiasm.sh
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hifiadapterfiltFCS.sh
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hic_yahs.sh
SH
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Complete Metadata
| @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", "title": "busco5.sh", "format": "sh", "mediaType": "text/x-shellscript", "downloadURL": "https://ndownloader.figshare.com/files/46146393" }, { "@type": "dcat:Distribution", "title": "genomescope2.sh", "format": "sh", "mediaType": "text/x-shellscript", "downloadURL": "https://ndownloader.figshare.com/files/46146396" }, { "@type": "dcat:Distribution", "title": "blob.sh", "format": "sh", "mediaType": "text/x-shellscript", "downloadURL": "https://ndownloader.figshare.com/files/46146399" }, { "@type": "dcat:Distribution", "title": "hifiasm.sh", "format": "sh", "mediaType": "text/x-shellscript", "downloadURL": "https://ndownloader.figshare.com/files/46146402" }, { "@type": "dcat:Distribution", "title": "hifiadapterfiltFCS.sh", "format": "sh", "mediaType": "text/x-shellscript", "downloadURL": "https://ndownloader.figshare.com/files/46146405" }, { "@type": "dcat:Distribution", "title": "hic_yahs.sh", "format": "sh", "mediaType": "text/x-shellscript", "downloadURL": "https://ndownloader.figshare.com/files/46146408" } ] |
| 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 | 2026-05-26 |
| programCode |
[ "005:040" ] |
| publisher |
{ "name": "Agricultural Research Service", "@type": "org:Organization" } |
| temporal | 2024-05-02/2024-05-02 |
| title | Bombus huntii genome assembly scripts |
