Kevin's repositories
2018-paper-spacegraphcats
Paper text and pipeline for "Exploring neighborhoods in large metagenome assembly graphs..."
2021-GGG298
Winter 2021, GGG 298 - Tools for Data Intensive Research - UC Davis
2022-GGG201b-lab
GGG 201(b), Intro to Bioinformatics - lab section. Winter 2022 at UC Davis.
2022-GGG298
Winter 2022 - Tools for Data Intensive Research at UC Davis.
angsd-snakemake
Example snakemake repo for NGS analysis pipeline
biotools
Standalone scripts that are useful for manipulating and analysing DNA sequence data
coding_excercises
A public repo of coding exercises
GAAS
Genome Assembly and Annotation Service code
genomics_general
General tools for genomic analyses.
LongRead_tutorials
Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
mitogenomics
Pyhton Scripts to annotate mitochondrial genomes
ML_medbioinfo
Machine Learning in Medical Bioinformatics
ngs-analysis
Various scripts for sequencing data analysis
Online_R_learning
Online R learning for applied statistics
ont-assembly-polish
ONT assembly and Illumina polishing pipeline
ont_tutorial_basicqc
A bioinformatics tutorial demonstrating a best-practice workflow to review a flowcell's sequence_summary.txt
orthosnake
snakemake script for orthology inference (prokka, orthofinder)
RASflow
RNA-Seq analysis workflow
rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
smsk_selection
Snakemake project to predict orthogroups and find patterns of postive selection with orthofinder and fastcodeml
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
training-collection
Collection of bioinformatics training materials
tutorials-1
Tutorials on phylogenomic analyses for the ForBio Phylogenomics course