USDA-ARS-GBRU/q2_itsxpress

This repository has been archived on 19/Dec/2023
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USDA-ARS-GBRU/q2_itsxpress

USDA-ARS-GBRU

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A plugin for qiime2 that runs ITSxpress

PanPipes

Test sets and pipeline scripts for pan-genomic graph analysis

metagenomics

Tutorial for Metagenomics Analyses

itsxpress

Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis

GuideMaker

GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes

vica

Vica: Software to identify highly divergent DNA and RNA viruses and phages in microbiomes

QTLsurge

Software for iterative genotyping design in a QTL-seq experiment

Grass_annotation_pipeline

crossword

branchwater-web

web app for search of SRA with Mastiff

itsxpress-tutorial

A tutorial for the QIIME2 forum

ml-training-site

Website for the USDA-ARS / UF Machine Learning Training 2019

Jupyter Notebook

GEERU_workshop

thoe 2024 GEERU/MSU scoping workshop in Starkville, MS

tamipami

A tool for finding the TAM and PAM sites of new Cas and transposon endonucleases from NGS screens

PeeDeeCottonBreedingProgram_Diversity

Supplemental materials for Billings et al *G3* (2021).

Ssec_Raleigh

Developing reference genome assembly for Stenotaphrum secundatum cultivar Raleigh

Citrus_GCMS

GC-MS analysis for citrus high throughput identification of knowns

HaploStrata

R app for viewing haplotype change over time

US_rice

Key programs/scripts used in manuscript "Gene disruption by structural mutations drives selection in US rice breeding over the last century"

Virginia-Type_Peanut_Genomic_Tool_Development

GuideMaker_paper

Scripts to parse timelogs from slurm and generate performance graphics

wiv_protein_domain

An analysis to find metagenomic instances of the WIV insect viral protein domain