jguhlin

Plant Genomicist and Bioinformatician interested in structural variation and pangenomics.

Dunedin, New Zealand

Pinned Repositories

Kakapo
Scripts and code for Kākāpō genomic data
Language:Jupyter Notebook14 10 01
beaker
Language:Jupyter Notebook3 4 10
biotools
Bio* library for Clojure, with a focus on reducers and parallelism support
Language:Clojure4 4 00
lostruct-py
Language:Jupyter Notebook8 4 82
minimap2-rs
Rust bindings to minimap2 library
Language:Rust72 7 3815
nanopore-basecaller-training
Experiments on training the nanopore basecaller (bonito -> guppy is the goal)
Language:Shell7 3 11
ODG
ODG: Omics Database Generator - Integration toolkit for -omics data
Language:Clojure8 4 04
sfasta
sfasta
Language:Rust35 5 30
syncmers
Library for finding syncmers from &[u8] in rust
Language:Rust6 2 02
useful-nextflow-patterns
Useful nextflow patterns and examples
Language:Nextflow3 4 01

jguhlin's Repositories

jguhlin/lostruct-py
Language:Jupyter Notebook8 4 82
jguhlin/syncmers
Library for finding syncmers from &[u8] in rust
Language:Rust6 2 02
jguhlin/useful-nextflow-patterns
Useful nextflow patterns and examples
Language:Nextflow3 4 01
jguhlin/Conservation_Genomics_The_Book
Book for Practical aspects of Conservation Genomics
Language:JavaScript2 2 0
jguhlin/acc2tax
acc2tax
Language:Rust1 2 0
jguhlin/AnnoSINE
SINE annotation tool for plant genomes
Language:Python1 1 0
jguhlin/bptree
Basic B+ Tree for use in SFASTA (and possibly elsewhere)
Language:Rust1 2 0
jguhlin/bytelines
Read input lines as byte slices for high efficiency
Language:Rust1 1 0
jguhlin/ffforf
Language:Rust1 3 01
jguhlin/fffx
Yet another fasta/x/q file parser
Language:Rust1 2 0
jguhlin/genome-annotation-guide
Language:Makefile1 2 0
jguhlin/kmer-generator
Language:Rust1
jguhlin/miniprot-rs
Miniprot Rust Bindings
Language:Rust1 3 01
jguhlin/Nextflow_Workshop
A workshop to help you integrate Nextflow in your analysis workflows for reproducible and scalable pipelines.
Language:HTML1 1 0
jguhlin/AGM-workshop-2023
Reproducibility with Nextflow and nf-core, structured for the one-day AGM training day workshop
Language:HTML1 0
jguhlin/alen
Simple terminal alignment viewer
Language:Rust0 0
jguhlin/AnnoQC
Potential project space for performing QC of Genome Annotations
Language:JavaScript2 0
jguhlin/bevy
A refreshingly simple data-driven game engine built in Rust
Language:Rust1 0
jguhlin/biobeaker_testing
Testing biobeaker models!
Language:Jupyter Notebook
jguhlin/gbwt-rs
GBWT in Rust
Language:Rust1 0
jguhlin/genomealign
Language:Nextflow2 0
jguhlin/jguhlin.github.io
Language:HTML3 0
jguhlin/ld54-limited-space
Ludum Dare 54 - Limited Space
Language:Rust2 0
jguhlin/medaka
Sequence correction provided by ONT Research
Language:Python1 0
jguhlin/my-test-repo
2 0
jguhlin/ReadStats
Language:Rust2 0
jguhlin/Toreador
Language:Rust2 0
jguhlin/toxicmethyl
Language:Rust2 0
jguhlin/typst-invoice
A Typst template for generating invoices
Language:Nix1 0
jguhlin/xorf
Xor filters - efficient probabilistic hashsets. Faster and smaller than bloom and cuckoo filters.
Language:Rust1 0