Pinned Repositories
abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
ABRicate_to_prokka
Match ABRicate hits to Prokka locus tags based on contig names and locations
assembly_snptyper
Type assembly based on a VCF using minimap2 + samtools
benchmark_SIGNL
Repository for the pipeline used in the SIGNL benchmark
benchmarking-refseq
extract_genes_ABRicate
Small script to use ABRicate output to extract genes from genome assemblies, reverse complement if necessary, and print to a file
itolparser
Small script to produce iTOL colorstrip metadata files from a table
pacbio_methylation_snakemake
Small pipeline to call methylation in Streptococcus suis using standard PacBio tools
snakemake_lisa
Test repository for running Snakemake on Lisa
Ssuis_genomic_epidemiology
Repo with Snakemake pipeline to analyse genomic epidemiology data of European Streptococcus suis whole-genome sequencing data
boasvdp's Repositories
boasvdp/itolparser
Small script to produce iTOL colorstrip metadata files from a table
boasvdp/extract_genes_ABRicate
Small script to use ABRicate output to extract genes from genome assemblies, reverse complement if necessary, and print to a file
boasvdp/assembly_snptyper
Type assembly based on a VCF using minimap2 + samtools
boasvdp/pacbio_methylation_snakemake
Small pipeline to call methylation in Streptococcus suis using standard PacBio tools
boasvdp/Ssuis_genomic_epidemiology
Repo with Snakemake pipeline to analyse genomic epidemiology data of European Streptococcus suis whole-genome sequencing data
boasvdp/abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
boasvdp/ABRicate_to_prokka
Match ABRicate hits to Prokka locus tags based on contig names and locations
boasvdp/bioconda-recipes
Conda recipes for the bioconda channel.
boasvdp/boasvdp
boasvdp/boasvdp.github.io
Personal website
boasvdp/boasvdp.github.io_backup
boasvdp/COMBAT
Snakemake pipeline for the analysis of COMBAT data
boasvdp/CSIS
Code Safety Inspection Service
boasvdp/GAS_M4
Snakemake pipeline to analyse genomic data of Streptococcus pyogenes M4
boasvdp/irods_rename
Rename files from an iRODS collection
boasvdp/juno-assembly
Pipeline to process raw sequencing data up to de-novo assembly and the accompanying statistics
boasvdp/match_chewBBACA_to_Enterobase
Scripts to match chewBBACA output to Enterobase cgMLST and hierarchical CCs
boasvdp/MedMicro_2020-2021_public
boasvdp/mlst_to_phyloviz
Small script to convert output from tseemann/mlst to allelic profile data for PhyloViz, with some extra checks
boasvdp/MRA_Streptococcus_suis
Repository for the Microbiology Resource Announcements paper on five complete Streptococcus suis genomes
boasvdp/nanopore_methylation_R9
(Pseudo)code for ONT de novo methylation analysis
boasvdp/network_analysis_scripts
Collection of network analysis scripts for ANI and/or SNP data
boasvdp/PIRATE
A toolbox for pangenome analysis and threshold evaluation.
boasvdp/pyelonephritis
Snakemake pipeline to link urine metagenomic sequencing data from pyelonephritis patients to cultured sepsis isolates
boasvdp/snakemake_playground
Test repo to use snakemake modules
boasvdp/snp-dists
Pairwise SNP distance matrix from a FASTA sequence alignment
boasvdp/submission_checklist
boasvdp/test_docs
Test mkdocs github pages
boasvdp/test_ghcr
boasvdp/test_new_juno_library