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:Jupyter Notebook90 7 4315
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/ODG
ODG: Omics Database Generator - Integration toolkit for -omics data
Language:Clojure8 4 04
jguhlin/biotools
Bio* library for Clojure, with a focus on reducers and parallelism support
Language:Clojure4 4 00
jguhlin/repeat-element-analysis
Commands, Scripts, and custom Programs used to analyze repeat elements in a forthcoming publication
Language:Shell1 3 0
jguhlin/3wasps
jguhlin/augustus
AUGUSTUS v3.2.1 for installation on Mac OS X
Language:C++3 0
jguhlin/binf-file-processor
Bioinformatics File Processor / Analyzer -- Examines files to see if they can form a continuous, connected network. Plan to use this for ODG auto-configuration and file testing.
Language:Clojure3 0
jguhlin/clj-btable
A binary serialization format for sparse, labeled 2D numeric datasets
Language:Clojure3 0
jguhlin/drake
Data workflow tool, like a "Make for data"
Language:Clojure
jguhlin/finalfrontier
Context-sensitive word embeddings with subwords. In Rust.
Language:Rust2 0
jguhlin/finalfusion-rust
finalfusion embeddings in Rust
Language:Rust
jguhlin/gene-ontology-db-example
gene-ontology-db-example
Language:Clojure3 0
jguhlin/genevalidator
GeneValidator: Identify problems with predicted genes
Language:Ruby
jguhlin/gf-targeted-prediction
Targeted gene family prediction using AUGSTUS-PPX, Nextflow, exonerate, etc...
Language:Nextflow3 0
jguhlin/git-collaboration
A repository to demonstrate collaboration workflows
jguhlin/ld-anchoring
Tool for improving genome assembly by anchoring contigs with population data (using LD)
Language:Clojure
jguhlin/nextflow-training
Language:Roff2
jguhlin/nf-select-best-model
Language:Clojure3 0
jguhlin/nn-replicon-identification
Neural Net to identify which replicon a sequence belongs to -- playground more than anything at this time
Language:Jupyter Notebook3 0
jguhlin/pacbio-paper-code
Language:Pep8
jguhlin/pangenome
Pan-genome Construction Software -- Under development
Language:Clojure1
jguhlin/SameSpeciesLiftover_nf
Same Species Liftover pipeline implemented in Nextflow
Language:Nextflow
jguhlin/spaln
Genome mapping and spliced alignment of cDNA or amino acid sequences
Language:C3 0
jguhlin/split-into-kmers
Language:Rust2 0
jguhlin/vespula_paper

jguhlin

Pinned Repositories

Kakapo

beaker

biotools

lostruct-py

minimap2-rs

nanopore-basecaller-training

ODG

sfasta

syncmers

useful-nextflow-patterns

jguhlin's Repositories

jguhlin/ODG

jguhlin/biotools

jguhlin/repeat-element-analysis

jguhlin/3wasps

jguhlin/augustus

jguhlin/binf-file-processor

jguhlin/clj-btable

jguhlin/drake

jguhlin/finalfrontier

jguhlin/finalfusion-rust

jguhlin/gene-ontology-db-example

jguhlin/genevalidator

jguhlin/gf-targeted-prediction

jguhlin/git-collaboration

jguhlin/ld-anchoring

jguhlin/nextflow-training

jguhlin/nf-select-best-model

jguhlin/nn-replicon-identification

jguhlin/pacbio-paper-code

jguhlin/pangenome

jguhlin/SameSpeciesLiftover_nf

jguhlin/spaln

jguhlin/split-into-kmers

jguhlin/vespula_paper