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/minimap2-rs
Rust bindings to minimap2 library
Language:Rust72 7 3815
jguhlin/sfasta
sfasta
Language:Rust35 5 30
jguhlin/beaker
Language:Jupyter Notebook3 4 10
jguhlin/fffx-tools
Simple utils for cleaning up FASTX files
Language:Rust1 2 0
jguhlin/fishtank
Fishtank: Manage your Nanopore Sequencing and Basecalling <*((((>< <*((((><
Language:Rust1
jguhlin/needletail
Fast FASTX parsing and k-mer methods in Rust
Language:Rust1 1 0
jguhlin/oracular
Language:Rust0 4 180
jguhlin/bevybio_sequence_widget
Language:Rust
jguhlin/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell0 0
jguhlin/bonito
A PyTorch Basecaller for Oxford Nanopore Reads
Language:Python0 0
jguhlin/burn
Burn is a new comprehensive dynamic Deep Learning Framework built using Rust with extreme flexibility, compute efficiency and portability as its primary goals.
jguhlin/darwin-core-to-rerun
Language:Rust
jguhlin/earthrs-modis
Rust bindings for MODIS Data
Language:Rust1 0
jguhlin/EDTA
Extensive de-novo TE Annotator
Language:Perl2 61
jguhlin/fav
jguhlin/hdf-eos2-rs
Language:C1 0
jguhlin/hdf-eos5-rs
Language:C1 0
jguhlin/herro
HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).
Language:Rust0 0
jguhlin/KGD
Kinship (genetic relatedness) using GBS (genotyping-by-sequencing) with Depth adjustment
Language:R1 0
jguhlin/kmer-embeddings
todo
Language:Rust
jguhlin/ldjam55
Language:Rust
jguhlin/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
jguhlin/nocroissants
Language:Rust1 0
jguhlin/nxf-components
Developmental Nextflow DSL2 components
Language:Nextflow0 0
jguhlin/oarfish
long read RNA-seq quantification
jguhlin/OxidMAF
Rust-driven MAF Tools
Language:Rust2 0
jguhlin/pangenome-prep
Language:Jupyter Notebook2 0
jguhlin/rerun-earth
Language:Rust1 0
jguhlin/taxotango
Language:Rust1 0
jguhlin/yazi
💥 Blazing fast terminal file manager written in Rust, based on async I/O.