stajichlab/general-genomics-tools

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Created about 11 years ago
Updated about 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)

REPET-slurm

SLURM-ready bash scripts to run the complete REPET pipeline

MojaveCrusts_2019analysis

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

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

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.

PopGenomics_template

Template for Population Genomics variant calling

Yugueros_cellwall_fungiphylogeny

Phylogenomic analysis for cell wall composition profiling

RNASeq_Bd_McDonald2020

Reanalysis of McDonald et al. 2020

ElkDung_GenomeAnnotation

Annotate Elk Dung associated fungal genomes

Afumigatus_RefStrains

Reference A. fumigatus strain panel

Tumor_mycobiome_2022

Tumor Mycombiome Project