Bombus huntii genome assembly scripts

<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>

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