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Alex Leonard's Projects

advntr icon advntr

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data

canu icon canu

A single molecule sequence assembler for genomes large and small.

clair3 icon clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

cramino icon cramino

A *fast* tool for BAM/CRAM quality evaluation, intended for long reads

danbing-tk icon danbing-tk

Toolkit for VNTR genotyping and repeat-pan genome graph construction

gfatk icon gfatk

A plant organellar Graphical Fragment Assembly toolkit

jupiterplot icon jupiterplot

A Circos-based tool to visualize genome assembly consistency

kapaluavisibility icon kapaluavisibility

A basic attempt to use satellite imagery to detect good conditions in Kapalua bay

minigraph icon minigraph

Proof-of-concept seq-to-graph mapper and graph generator

odgi icon odgi

Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs (https://doi.org/10.1093/bioinformatics/btac308)

pggb icon pggb

the pangenome graph builder

polyomino_core icon polyomino_core

Central repository for the lattice polyomino self-assembly model

polyomino_duplication icon polyomino_duplication

Polyomino self-assembly study of duplication and evolution of structural complexity in proteins.

pyfaidx icon pyfaidx

Efficient pythonic random access to fasta subsequences

qtltools icon qtltools

A complete tool set for molecular QTL discovery and analysis

repeatmasker icon repeatmasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

scuba icon scuba

Just some fun visualising scuba diving data

slam icon slam

Square Lattice Assembly Model

snakemake icon snakemake

This is the development home of the workflow management system Snakemake. For general information, see

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