stajichlab/general-genomics-tools

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Created over 11 years ago
Updated over 11 years ago

stajichlab/general-genomics-tools

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General purpose tools for genomics tools for the lab used in publications.

OrthoMCL

AAFTF

Automatic Assembly For The Fungi

FGMP

Fungal Genome Mapping Pipeline

biosample_metadata

Extract metadata from biosamples in NCBI

Comparative_pipeline

Comparative genomics pipeline

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)

MojaveCrusts_2019analysis

This is repo for Mojave crusts analysis including 16S and ITS data from GMT, KELSO, CIMA, and JTNP

REPET-slurm

SLURM-ready bash scripts to run the complete REPET pipeline

GenoAnnoFlow

Genome annotation pipeline and Visualization

GenomeAnnotation

Description of Genome Annotation Procedures

Chytrid_Coelomomyces_Project

C_lusitaniae_popseq

Genomic analyses of Clavispora (Candida) lusitaniae strains

labmeeting-snippets

Lab meeting code review and examples

Microbiome_resources

Microbiome tools and resources for Stajichlab projects

RelocaTE3

ReLocaTE code for identifying Transposons (TE) in genomes using re-sequencing data

Dynamic_rice_publications

PopGenomics_template

Template for Population Genomics variant calling

Rice_RILs_PopA123_EG4

EG4xA123 RIL population analysis

neurospora_MSUD

Neurospora MSUD project

KassonLab_OphiocordycepsSymbiont

Ophiocordyceps symbiont genomes project with Matt Kasson lab (WVU)

localizaTE

de novo and homology based Transposable Element annotation system

GWSS_Genome

Jupyter Notebook

rozella

Rozella genome project

Hortaea_werneckii

Hortea experimental evolution and reannotation project

Workshop_Rplotting

Lab R tutorials

Microbiome_Nicole_Jornada

Microbiome analysis for Nicole's data from Jornada(NMSU). Currently, these data are from Flowcell913(16S) at UCR.

Yugueros_cellwall_fungiphylogeny

Phylogenomic analysis for cell wall composition profiling

RNASeq_Bd_McDonald2020

Reanalysis of McDonald et al. 2020

Antarctic_Virus_Discovery

ElkDung_GenomeAnnotation

Annotate Elk Dung associated fungal genomes

Afumigatus_RefStrains

Reference A. fumigatus strain panel

Tumor_mycobiome_2022

Tumor Mycombiome Project