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OrthoMCL
AAFTF
Automatic Assembly For The FungiFGMP
Fungal Genome Mapping Pipelinebiosample_metadata
Extract metadata from biosamples in NCBIComparative_pipeline
Comparative genomics pipelinePHYling
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)MojaveCrusts_2019analysis
This is repo for Mojave crusts analysis including 16S and ITS data from GMT, KELSO, CIMA, and JTNPREPET-slurm
SLURM-ready bash scripts to run the complete REPET pipelineGenoAnnoFlow
Genome annotation pipeline and VisualizationGenomeAnnotation
Description of Genome Annotation ProceduresC_lusitaniae_popseq
Genomic analyses of Clavispora (Candida) lusitaniae strainslabmeeting-snippets
Lab meeting code review and examplesMicrobiome_resources
Microbiome tools and resources for Stajichlab projectsRelocaTE3
ReLocaTE code for identifying Transposons (TE) in genomes using re-sequencing dataDynamic_rice_publications
PopGenomics_template
Template for Population Genomics variant callingRice_RILs_PopA123_EG4
EG4xA123 RIL population analysisneurospora_MSUD
Neurospora MSUD projectKassonLab_OphiocordycepsSymbiont
Ophiocordyceps symbiont genomes project with Matt Kasson lab (WVU)localizaTE
de novo and homology based Transposable Element annotation systemGWSS_Genome
rozella
Rozella genome projectHortaea_werneckii
Hortea experimental evolution and reannotation projectWorkshop_Rplotting
Lab R tutorialsMicrobiome_Nicole_Jornada
Microbiome analysis for Nicole's data from Jornada(NMSU). Currently, these data are from Flowcell913(16S) at UCR.general-genomics-tools
General purpose tools for genomics tools for the lab used in publications.Yugueros_cellwall_fungiphylogeny
Phylogenomic analysis for cell wall composition profilingRNASeq_Bd_McDonald2020
Reanalysis of McDonald et al. 2020Antarctic_Virus_Discovery
ElkDung_GenomeAnnotation
Annotate Elk Dung associated fungal genomesAfumigatus_RefStrains
Reference A. fumigatus strain panelTumor_mycobiome_2022
Tumor Mycombiome ProjectLove Open Source and this site? Check out how you can help us