USDA-ARS Genomics and Bioinformatics Research Unit
- 45 followers
- United States of America
- https://www.ars.usda.gov/southeast-area/stoneville-ms/genomics-and-bioinformatics-research/
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Repositories
- genotype-assembly2snpchip Public
Generic 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.
USDA-ARS-GBRU/genotype-assembly2snpchip’s past year of commit activity - SugarcaneIndustryCrossingTool Public Forked from USDA-ARS-GBRU/SugarcaneCrossingTool
customizations requested by stakeholders
USDA-ARS-GBRU/SugarcaneIndustryCrossingTool’s past year of commit activity - SugarcaneCrossingTool Public
USDA-ARS-GBRU/SugarcaneCrossingTool’s past year of commit activity - 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.
USDA-ARS-GBRU/breedbase-image-analysis-module’s past year of commit activity - 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.
USDA-ARS-GBRU/Panex_Privus’s past year of commit activity - salmonella_genome_assembly Public
a Nextflow workflow for assembling Salmonella genomes on a SLURM HPC using apptainer
USDA-ARS-GBRU/salmonella_genome_assembly’s past year of commit activity - 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.
USDA-ARS-GBRU/BLAST_primer_filter’s past year of commit activity - HiFi-Genome-Assembly Public
Beginner-friendly workflow for PacBio HiFi genome assembly, from raw reads to polished contigs and quality assessment. A practical bioinformatics protocol with clear steps, commands, tool choices, HPC tips, and best practices for students learning modern long-read genome assembly.
USDA-ARS-GBRU/HiFi-Genome-Assembly’s past year of commit activity - Hole-Punch-Tube-Adapter-Modified-Design- Public
This design is a modification of the original hole punch tube adapter developed by the Rife Lab. It enables direct collection into 8-well strip tubes, eliminating the need to manually cut and separate tubes prior to sampling.
USDA-ARS-GBRU/Hole-Punch-Tube-Adapter-Modified-Design-’s past year of commit activity
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