Jason Stajich Lab at UC Riverside
Evolutionary Genomics of Fungi projects, data and software
RIverside, CA
Pinned Repositories
AAFTF
Automatic Assembly For The Fungi
biosample_metadata
Extract metadata from biosamples in NCBI
Comparative_pipeline
Comparative genomics pipeline
FGMP
Fungal Genome Mapping Pipeline
funannotate_template
Project template for doing a funannotate annotation set
OrthoMCL
PHYling
Unified PHYling pipeline for species tree building from annotated genomes (see https://github.com/stajichlab/AAFTF and https://github.com/nextgenusfs/funannotate for assembly and annotation steps)
PopGenomics_template
Template for Population Genomics variant calling
RelocaTE2
This tool is for mapping TEs from resequencing data: Stajich lab
SOP_data
Standard Operating Procedures
Jason Stajich Lab at UC Riverside's Repositories
stajichlab/GWSS_Genome
stajichlab/Hortaea_werneckii
Hortea experimental evolution and reannotation project
stajichlab/Tumor_mycobiome_2022
Tumor Mycombiome Project
stajichlab/funannotate_template
Project template for doing a funannotate annotation set
stajichlab/GWSS_Resistance
stajichlab/SOP_data
Standard Operating Procedures
stajichlab/.github
stajichlab/Afumigatus_pangenome
A. fumigatus pangenome analyses
stajichlab/Antarctica_Tuscia_CCFEE_202205
Antarctic and CCFEE strain genomes
stajichlab/AsmAnnot_Aspergillus_melleus_IMV_01140
Tools to support assembly and annotation for Aspergillus melleus IMV 01140
stajichlab/Asocialis_CCGP_metagenome
Metagenome processing for the Acarospora socialis population sampling
stajichlab/Bd_popgenomics_assemblies
Assembly, Metagenome analyses of Bd population sequencing
stajichlab/BlackYeast_JES119_genome
Genome seq for JES119 strain
stajichlab/CASIS_PopGen
re-run of CASIS dataasets
stajichlab/Chytrid_Coelomomyces_RNASeq
Run RNAseq on Coelomomyces
stajichlab/CIFAR4D_Subsurface_Test
Test set of 3 subsurface filter for Fungi
stajichlab/EntoGenomes_Methylation
stajichlab/git-github-tutorial
Git and GitHub tutorial for NSURP 2022. This repo would be used to practice fork and pull requests function.
stajichlab/GWSS_Resistance_MAGs
stajichlab/KassonLab_Cryphonectria
Cryphonectria genomes project with Matt Kasson lab (WVU)
stajichlab/lab_coding_workshops
Lab workshops on coding proficiency
stajichlab/mcclintock
Meta-pipeline to identify transposable element insertions using next generation sequencing data
stajichlab/Ophidiomyces_ophiodiicola_Population_Annotation
Annotation of the snake fungal disease O.ophiodiicola genome assemblies
stajichlab/PopGenomics_Acarospora_socialis_HerbariumSamples
Population genomics of A. socialis from Herbarium specimens
stajichlab/PopGenomics_Cimmitis_WAref
Population Genomics of C. immitis using WA211 as ref
stajichlab/PopGenomics_Cposadasii
C.posa variant calling and CNV exploration using
stajichlab/PopGenomics_Elasticomyces_elasticus
Population Genomics of E. elasticus
stajichlab/PopGenomics_Friedmanniomyces_endolithicus
Friedmanomyces endolithicus popgenomics
stajichlab/smk_genomeasm_illumina
Snakemake pipeline for Illumina only data, using AAFTF and others
stajichlab/UCcolors
Color palette for Univ of California school colors