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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

fastix icon fastix

Prefix-renaming FASTA records really fast.

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

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