Pinned Repositories
Phylign
Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on a laptop within a few hours.
BacQuerya
Search engine for bacterial genomic information.
BacQuerya-api
Backend API for the BacQuerya web app.
BacQuerya-processing
Scripts to process publicly available information for indexing.
AllTheBacteria
Follow up to Grace Blackwell's 661k dataset, for 2023
approximate-cluster-identities
A python package to visualise the approximate within and between cluster identities of a large number of short sequences.
artic-ncov2019
ARTIC nanopore protocol for nCoV2019 novel coronavirus
primers-containers
A repository for tasks to complete in the containers session of primers for predocs 2023.
viridian_simulations_workflow
Workflow to simulate SARS-CoV-2 amplicons and reads.
CRISPR-TAPE
A protein-centric CRISPR gRNA design tool for TArgeted Protein Engineering: please cite Anderson&Benns et al (2020) Mol Syst Biol (2020)16:e9475
Danderson123's Repositories
Danderson123/primers-containers
A repository for tasks to complete in the containers session of primers for predocs 2023.
Danderson123/AllTheBacteria
Follow up to Grace Blackwell's 661k dataset, for 2023
Danderson123/approximate-cluster-identities
A python package to visualise the approximate within and between cluster identities of a large number of short sequences.
Danderson123/artic-ncov2019
ARTIC nanopore protocol for nCoV2019 novel coronavirus
Danderson123/bioconda-recipes
Conda recipes for the bioconda channel.
Danderson123/fieldbioinformatics
The ARTIC field bioinformatics pipeline
Danderson123/dingII
Mirror of https://gitlab.ub.uni-bielefeld.de/gi/dingiiofficial
Danderson123/Masters_Project
Danderson123/ncov2019-artic-nf
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
Danderson123/panaroo
An updated pipeline for pangenome investigation
Danderson123/pandora
Pan-genome inference and genotyping with long noisy or short accurate reads
Danderson123/personal-site
Danderson123/PopPUNK
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
Danderson123/snip-public
SNIP: SINGLE-SHOT NETWORK PRUNING BASED ON CONNECTION SENSITIVITY
Danderson123/SNP_simulator
Simulate SNPs across a phylogenetic tree using a reference.