Pinned Repositories
bigsi_rs
Rust in-memory implementation of a BIGSI-like data structure
colorid
Experiments with using BIGSI data structure for metagenomic and QC applications
colorid_bv
Colorid using a new BIGSI implementation
fastbloom
A fast bloom filter implemented by Rust for Python! 10x faster than pybloom!
GTDB_Kraken
Kraken(2) database based on the GTDB project
mcOutbryk
SNP calling pipeline using mccortex
N50.sh
bash script to quickly produce some assembly stats
phylo_misbehave
SalmID
Rapid confirmation of Salmonella spp. and subspp. from sequence data
sepia
taxonomic classifier based on the kraken2 algorithms and more
hcdenbakker's Repositories
hcdenbakker/sepia
taxonomic classifier based on the kraken2 algorithms and more
hcdenbakker/GTDB_Kraken
Kraken(2) database based on the GTDB project
hcdenbakker/colorid
Experiments with using BIGSI data structure for metagenomic and QC applications
hcdenbakker/bigsi_rs
Rust in-memory implementation of a BIGSI-like data structure
hcdenbakker/SalmID
Rapid confirmation of Salmonella spp. and subspp. from sequence data
hcdenbakker/phylo_misbehave
hcdenbakker/N50.sh
bash script to quickly produce some assembly stats
hcdenbakker/colorid_bv
Colorid using a new BIGSI implementation
hcdenbakker/mcOutbryk
SNP calling pipeline using mccortex
hcdenbakker/fastbloom
A fast bloom filter implemented by Rust for Python! 10x faster than pybloom!
hcdenbakker/PySnpSites
Experiments optimising python (with Cython)
hcdenbakker/SeqSeroK
A k-mer based implementation of SeqSero
hcdenbakker/SRA_SeqSeroandIsPCR
pipeline for download, assembly and in silico PCR for primer testing in python
hcdenbakker/atlas
ATLAS - Three commands to start analysing your metagenome data
hcdenbakker/CheckM
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
hcdenbakker/ClonalFrameML
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
hcdenbakker/cortex
reference free variant assembly
hcdenbakker/fANI2Tree
A R script to create an ANI-based UPGMA tree from fastANI output
hcdenbakker/mockcommunity
Long-read mock community experiments
hcdenbakker/RetailBiofilmStudy
Rscripts and data for analyses of microbiota found in drains in retail delis
hcdenbakker/Scoary
Pan-genome wide association studies
hcdenbakker/SeqSero
Salmonella serotyping from genome sequencing data
hcdenbakker/SeqSero2
SeqSero2 alpha test
hcdenbakker/succession_fecal_microbiomes
hcdenbakker/treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
hcdenbakker/TreeToReads
Pipeline to generate NGS reads from a phylogeny