Alex Leonard's repositories
adVNTR
A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
BovinePangenome.github.io
Bovine Pan-Genome Consortium Website
bovLRC-documentation
Official documentation for BovLRC
calN50
Compute N50/NG50 and auN/auNG
canu
A single molecule sequence assembler for genomes large and small.
cramino
A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
danbing-tk
Toolkit for VNTR genotyping and repeat-pan genome graph construction
HIMB-Summer-Course-2019-Remote-Sensing-Imagery-Module-1-Measuring-Reefs-
Applying Innovative Technology in Marine Science: Remote Sensing Imagery component, Module 1
polyomino_core
Central repository for the lattice polyomino self-assembly model
Scuba
Just some fun visualising scuba diving data
Clair3
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
gfatk
A plant organellar Graphical Fragment Assembly toolkit
Jasmine
Jasmine: SV Merging Across Samples
JupiterPlot
A Circos-based tool to visualize genome assembly consistency
minigraph
Proof-of-concept seq-to-graph mapper and graph generator
odgi
Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs (https://doi.org/10.1093/bioinformatics/btac308)
pggb
the pangenome graph builder
polyomino_duplication
Polyomino self-assembly study of duplication and evolution of structural complexity in proteins.
pyfaidx
Efficient pythonic random access to fasta subsequences
qtltools
A complete tool set for molecular QTL discovery and analysis
RepeatMasker
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
snakemake
This is the development home of the workflow management system Snakemake. For general information, see
Sniffles
Structural variation caller using third generation sequencing