Name: Boas van der Putten
Type: User
Company: RIVM @RIVM-bioinformatics
Bio: Public health bioinformatician
Twitter: boasvdputten
Location: Bilthoven, the Netherlands
Blog: https://boasvdp.github.io/
Boas van der Putten's Projects
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
Match ABRicate hits to Prokka locus tags based on contig names and locations
Type assembly based on a VCF using minimap2 + samtools
Repository for the pipeline used in the SIGNL benchmark
Conda recipes for the bioconda channel.
Personal website
Snakemake pipeline for the analysis of COMBAT data
Code Safety Inspection Service
Small script to use ABRicate output to extract genes from genome assemblies, reverse complement if necessary, and print to a file
Snakemake pipeline to analyse genomic data of Streptococcus pyogenes M4
Small script to produce iTOL colorstrip metadata files from a table
Pipeline to process raw sequencing data up to de-novo assembly and the accompanying statistics
Scripts to match chewBBACA output to Enterobase cgMLST and hierarchical CCs
Small script to convert output from tseemann/mlst to allelic profile data for PhyloViz, with some extra checks
Repository for the Microbiology Resource Announcements paper on five complete Streptococcus suis genomes
(Pseudo)code for ONT de novo methylation analysis
Collection of network analysis scripts for ANI and/or SNP data
Small pipeline to call methylation in Streptococcus suis using standard PacBio tools
A toolbox for pangenome analysis and threshold evaluation.
Snakemake pipeline to link urine metagenomic sequencing data from pyelonephritis patients to cultured sepsis isolates
Test repository for running Snakemake on Lisa
Test repo to use snakemake modules
Pairwise SNP distance matrix from a FASTA sequence alignment
Repo with Snakemake pipeline to analyse genomic epidemiology data of European Streptococcus suis whole-genome sequencing data
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