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/Comparative_pipeline
Comparative genomics pipeline
stajichlab/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)
stajichlab/RelocaTE3
ReLocaTE code for identifying Transposons (TE) in genomes using re-sequencing data
stajichlab/PopGenomics_template
Template for Population Genomics variant calling
stajichlab/ElkDung_GenomeAnnotation
Annotate Elk Dung associated fungal genomes
stajichlab/RolshausenLab_Aspergillus_DatePalm
Aspergillus tubingensis DFA genome sequencing and annotation
stajichlab/Yugueros_cellwall_fungiphylogeny
Phylogenomic analysis for cell wall composition profiling
stajichlab/GWSS_Microbiome_Analysis
stajichlab/MATPredict
This repository is dedicated to the development of a tool that can predict MAT loci in fungi.
stajichlab/moss_mycobiome
Repository for all code related to moss biocrust mycobiome studies across an aridity gradient including AMF specific analyses and general fungal diversity.
stajichlab/Biocrust_fungi_hybrid_asm_annotation
Nanopore and illumina sequences for biocrust fungal isolates
stajichlab/Botrytis_sRNA_profile
Re-processing public sRNA data from Botrytis
stajichlab/Chytrid_Virus
Chytrid Virus finding
stajichlab/CIFAR_DeepUnderFungi_MG
Deep Underground Fungi Search
stajichlab/ExtremeRhodotorula_DraftGenomes
Draft genomes from short read data
stajichlab/find_ping_pong_JinfengPipeline
stajichlab/KassonLab_Nectriaceae
Nectriaceae genomes project with Matt Kasson lab (WVU)
stajichlab/KassonLab_Verticillium
Verticillium genomes project with Matt Kasson lab (WVU)
stajichlab/make_simulated_genome
stajichlab/Massospora_cicadina_MAGs
stajichlab/Ncrassa_mutant_analyses
Analysis of 500+ Classic Mutants
stajichlab/PopGenomics_Afumigatus_Global
A. fumigatus population genomics 2021 relaunch
stajichlab/PopGenomics_Bd
Batrachochytrium dendrobatidis run
stajichlab/PopGenomics_Cimmitis
Population Genomics and CNV analysis of C. immitis strains
stajichlab/PopGenomics_Rhodotorula_mucilaginosa_NRRLY2510
Rhodotorula mucilaginosa population genomics with ref strain NRRL Y-2510
stajichlab/stajichlab.github.io
Stajich Lab Website
stajichlab/stajichlab.github.io-v2
lab site test
stajichlab/TaniaK_CF_Exophiala_dermatitidis
Archiving repo from paper.
stajichlab/Trebouxia_Schmitt
Duplication analysis
stajichlab/Y1000_orthologs
Compare and Build Orthogroups for Y1000 dataset and compare to YGOB