Upalabdha's repositories
SequenceTools
Programs used in the lab for various tasks
ANIclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes using fastANI & seaborn
appliedgenomics2022
Materials for EN.601.449/EN.601.649 Computational Genomics: Applied Comparative Genomics
awesome-genome-visualization
A list of interesting genome browser or genome-browser-like implementations
awesome-nanopore
A curated list of awesome nanopore analysis tools.
assembly-stats
Assembly statistic visualisation
bioinfo_commandline_oneliners
Useful bash one-liners for bioinformatics.
circlator
A tool to circularize genome assemblies
compare_genomes
A comparative genomics workflow using Nextflow, conda, Julia and R
GATK_parallel
Development of short tutorials for UNM's Center for Advanced Research Computing
Gene-Synteny-Analysis
Uses MCscan (python version) to create micro- and macro-synteny plots
GGisy
Genome-Genome circle synteny
karyotypeR
Program for computing karyoytypes from aDNA data.
Orthofinder_to_CAFE_scripts
This contains custom scripts to process orthofinder output for CAFE5 analysis
phylogenomics_phylogentics_tutorials
Tutorials on phylogenetic and phylogenomic inference
pymodulon
Python package for analyzing and visualizing iModulons
score-assemblies
Score and compare multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
scRNA-seq_notes
A list of scRNA-seq analysis tools
snakemake-training
Increasingly complete example bioinformatics workflow
tidy-ncbi-genome-download
Collect and filter genomes downloaded using [ncbi-genome-downloa](https://github.com/kblin/ncbi-genome-download), change file names to safe names for down-stream processing (phylogenetic tree making etc.)
training-collection
Collection of bioinformatics training materials
UpalabdhaD.github.io
A beautiful, simple, clean, and responsive Jekyll theme for academics
vcfstats
Powerful statistics for VCF files