Pinned Repositories
1976
Visualisation of students killed by the police in 1976
1976_map_vue
Victims of the Apartheid state: 1976 map (current focus: Western Cape)
adjust_vcf
amplicon_schemes
count_constant_sites
cwltutorial
Examples to help in a Common Workflow Language tutorial
diamond_add_taxonomy
Tools for working with NCBI taxonomy database (and DIAMOND output)
lukasa
ncbitaxonomy
a Rust crate for working with a local copy of the NCBI Taxonomy database
parse_accessions
pvanheus's Repositories
pvanheus/count_constant_sites
pvanheus/ampseer
Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing library they are read from. It is intended to differentiate between ARTIC v3, ARTIC v4, ARTIC v4.1, VarSkip 1a, VarSkip 2, Midnight and VarSkip Long primer sets sequenced by Illumina or ONT.
pvanheus/auspice
Web app for visualizing pathogen evolution
pvanheus/baobab.lims
Baobab LIMS is an open-source laboratory information management system (LIMS)
pvanheus/bitc2019_notebooks
Jupyter notebooks from the BITC 2019 course
pvanheus/combattbworkbench-docs
pvanheus/compare_annotation
pvanheus/COSMO
A tool for detecting operons in microorganisms using RNA-seq data
pvanheus/cwl-v1.2
Released CWL v1.2 specification
pvanheus/hAMRonization
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
pvanheus/hpc-intro-2022
pvanheus/infrastructure-playbook
Ansible playbook for managing UseGalaxy.eu infrastructure. For the playbook managing Galaxy itself, see https://github.com/galaxyproject/usegalaxy-playbook/
pvanheus/irida
Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
pvanheus/irida-uploader
Sequence file uploader for IRIDA
pvanheus/lesotho_scripts
Scripts used at NRL Lesotho
pvanheus/monkeypox
Nextstrain build for monkeypox virus
pvanheus/multiSub
Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input directory and merges everything into a single output directory. Auto-detects input file formats. Can submit the results to multiple repositories from the command line.
pvanheus/ncov
Nextstrain build for novel coronavirus SARS-CoV-2
pvanheus/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
pvanheus/pathogen-profiler
This repository contains python classes and functions to quickly create a profiling tool for pathogen NGS data
pvanheus/pirate-get
A command line interface for The Pirate Bay
pvanheus/planets
pvanheus/pokay
Report salient qPCR primer/probe or immune epitope mismatches info against a set of pathogen isolate genomes
pvanheus/primer-schemes
Primer schemes for real-time genome epidemiology
pvanheus/primer-schemes-phacnml
Schemes for SarsCoV2 sequencing
pvanheus/sars-cov-2-workflow-comparison
A collection of workflows for analyzing the SARS-CoV-2 genome.
pvanheus/SARS-CoV-2_BEDs
BED files for various COVID primer panels. I am not the original author
pvanheus/TBProfiler
Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
pvanheus/user_documentation
Repository for all user facing documentation for SANBI and SANBI systems.
pvanheus/usher
Ultrafast Sample Placement on Existing Trees