Genomics software engineer at the Garvan Institute, Sydney. I build bioinformatics tools: file formats, signal processing, high performance analysis methods
Co-creator of SLOW5/BLOW5 (Nature Biotechnology), a high-performance alternative to ONT's FAST5/POD5 formats.
SquiggleKit nanopore raw signal toolkit
deeplexicon deep learning barcode demultiplexer for nanopore data
kuva scientific plotting library and CLI tool
slow5lib-rs Pure Rust library for the SLOW5/BLOW5 file format
pod5lib-rs Pure Rust library for the POD5 nanopore file format
svb streamVbyte in pure Rust with SIMD for u16/u32/u64 and delta/zigzag
bedpull Extract sequences from BAM, PAF, or FASTA files using BED coordinates
blue-crab Lossless nanopore pod5 <=> s/blow5 file conversion
buttery-eel A slow5 guppy/dorado basecaller wrapper
poa-consensus poa consensus library and cli
- SLOW5 (enduring advantages), GigaScience 2025 — 10.1093/gigascience/giaf118
- Squigualiser, Bioinformatics 2024 — 10.1093/bioinformatics/btae501
- Squigulator, Genome Research 2024 — 10.1101/gr.278730.123
- slow5curl, GigaScience 2024 — 10.1093/gigascience/giae016
- SLOW5 (accelerated basecalling), Bioinformatics 2023 — 10.1093/bioinformatics/btad352
- SLOW5/BLOW5, Nature Biotechnology 2022 — 10.1038/s41587-021-01147-4
- interARTIC, Bioinformatics 2022 — 10.1093/bioinformatics/btab846
- deeplexicon, Genome Research 2020 — 10.1101/gr.260836.120
- RAGE-seq, Nature Communications 2019 — 10.1038/s41467-019-11049-4
- SquiggleKit, Bioinformatics 2019 — 10.1093/bioinformatics/btz586
Mastodon · Bluesky · jmferguson.science
I know my code is weird. How else would I know it is mine?