Bombus huntii genome assembly scripts

workflow

posted on 2024-05-14, 16:41 authored by SHEINA SIMSHEINA SIM

<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>

Funding

USDA-ARS: 2040-22430-028-000-D

USDA-ARS: 0500-00093-001-00-D

National Science Foundation: DEB-2126418

National Science Foundation: DEB-2126417

USDA-ARS: 0201-88888-003-000D

USDA-ARS: 0201-88888-002-000D

History

Related Materials

1.
URL - Compiles Genome sequencing of Bombus huntii (Hunt bumble bee) adult haploid male
2.
DOI - Is supplement to Parys, K.A., Schweizer, R.M., Benavides, L., Geib, S.M., Sim, S.B., Evans, J.D. & Branstetter, M.G. (2025). Chromosome-level genome assembly of Protandrena (Anthemurgus) passiflorae (Hymenoptera: Andrenidae), a host-plant specialist bee. G3: Genes|Genomes|Genetics. https://doi.org/10.1093/g3journal/jkaf096
3.
DOI - Is supplement to Jonathan Berenguer Uhuad Koch, Sheina B Sim, Brian Scheffler, Jeffrey D Lozier, Scott M Geib, Chromosome-scale genome assembly of the hunt bumble bee, Bombus huntii Greene, 1860, a species of agricultural interest, G3 Genes|Genomes|Genetics, Volume 14, Issue 10, October 2024, jkae160, https://doi.org/10.1093/g3journal/jkae160
4.
URL - Requires bamtools v2.5.1
5.
URL - Requires pigz v2.6
6.
URL - Requires any2fasta v0.4.2
7.
URL - Requires Singularity v3.8.3
8.
URL - Requires NCBI FCS adaptor
9.
URL - Requires HiFiAdapterFilt v3.0.1
10.
URL - Requires HiFiASM v0.19.3-r572

Data contact name

Sim, Sheina B.

Data contact email

sheina.sim@usda.gov

Publisher

Ag Data Commons

Intended use

Supplement to manuscript.

Temporal Extent Start Date

2024-05-02

Theme

Non-geospatial

ISO Topic Category

biota

National Agricultural Library Thesaurus terms

genome assembly; North America; population genetics; breeding; genome; haploidy; chromosomes; chromosome number; Bombus terrestris;

OMB Bureau Code

005:18 - Agricultural Research Service

OMB Program Code

005:040 - National Research

ARS National Program Number

Primary article PubAg Handle

https://handle.nal.usda.gov/10113/9276546

Pending citation

Public Access Level

Public

Usage metrics

Keywords

genome assembly protocol genome assembly genome; chromosomes Bombus hunti Hunt bumble bee

Licence

CC BY-SA 4.0