Boas van der Putten's repositories
itolparser
Small script to produce iTOL colorstrip metadata files from a table
extract_genes_ABRicate
Small script to use ABRicate output to extract genes from genome assemblies, reverse complement if necessary, and print to a file
assembly_snptyper
Type assembly based on a VCF using minimap2 + samtools
pacbio_methylation_snakemake
Small pipeline to call methylation in Streptococcus suis using standard PacBio tools
Ssuis_genomic_epidemiology
Repo with Snakemake pipeline to analyse genomic epidemiology data of European Streptococcus suis whole-genome sequencing data
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
bioconda-recipes
Conda recipes for the bioconda channel.
boasvdp.github.io
Personal website
CSIS
Code Safety Inspection Service
GAS_M4
Snakemake pipeline to analyse genomic data of Streptococcus pyogenes M4
juno-assembly
Pipeline to process raw sequencing data up to de-novo assembly and the accompanying statistics
match_chewBBACA_to_Enterobase
Scripts to match chewBBACA output to Enterobase cgMLST and hierarchical CCs
mlst_to_phyloviz
Small script to convert output from tseemann/mlst to allelic profile data for PhyloViz, with some extra checks
MRA_Streptococcus_suis
Repository for the Microbiology Resource Announcements paper on five complete Streptococcus suis genomes
nanopore_methylation_R9
(Pseudo)code for ONT de novo methylation analysis
network_analysis_scripts
Collection of network analysis scripts for ANI and/or SNP data
PIRATE
A toolbox for pangenome analysis and threshold evaluation.
pyelonephritis
Snakemake pipeline to link urine metagenomic sequencing data from pyelonephritis patients to cultured sepsis isolates
snakemake_playground
Test repo to use snakemake modules
snp-dists
Pairwise SNP distance matrix from a FASTA sequence alignment