USDA-ARS Genomics and Bioinformatics Research Unit
- 46 followers
- United States of America
- https://www.ars.usda.gov/southeast-area/stoneville-ms/genomics-and-bioinformatics-research/
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Repositories
- SugarcaneIndustryCrossingTool Public Forked from USDA-ARS-GBRU/SugarcaneCrossingTool
customizations requested by stakeholders
- itsxpress Public
Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis
- Okra_genome_assembly Public
- Panex_Privus Public
Find genomic variants shared within your target group and absent from everything else. A pangenome analysis. Requires multiple whole genome assemblies for target and non-target phenotypes.
- breedbase-image-analysis-module Public
A standardized, API-driven backend framework for integrating automated image analysis pipelines into BreedBase, enabling reproducible extraction of image-derived phenotypes, quality control metrics, and provenance metadata for use in breeding programs.
- genotype-assembly2snpchip Public
Workflow for validating genome assembly identities against SNP-chip or marker-panel VCFs using minimap2, bcftools targeted genotyping, gtcheck summaries, and student-friendly documentation for any crop/HPC.
- SugarcaneCrossingTool Public
- salmonella_genome_assembly Public
a Nextflow workflow for assembling Salmonella genomes on a SLURM HPC using apptainer
- BLAST_primer_filter Public Forked from rotheconrad/BLAST_primer_filter
A Python tool for screening primer pairs against genome BLAST results, reporting viable amplicons, failed hits, GFF3 annotations, and genome-wide PDF plots.
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