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abaumannii-pangenome

abeellab.github.io

afterqc

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

alpaca

Alpaca is a stand-alone method for identifying mosaic events in microbial genomes.

aneusim

A tool to generate synthetic aneuploid and polyploid genomes

ara

atk

Abeel Toolkit is set of utility classes that are used in our other projects.

bluejay

colldr

Rapid TB drug resistance determination from NGS data

course_bioinformatics1819

Course repository for Bioinformatics (NB2161) 2018-2019

cs4255

Course material for the Algorithms for sequence-based bioinformatics course (CS4255) at TU Delft

ctag

Graph genome browser

emu

Emu is a tool that canonicalizes non-identical representations of large insertions and deletions (indels) and substitutions across multiple genome samples.

genometools

GenomeTools is a collection of algorithms to manipulate genomics related file format. The primary purpose is to convert file formats from one to another.

graphclean

Assembly graph cleaning through machine learning improves de novo long-read assembly

graphlift

hadeda

hat

Haplotype Assembly Tool

integrated_bioinformatics

javaml

Java Machine Learning Library

kmertree

Approximate tree building with kmers

labdocuments

Documents supporting the lab

long-read-assembly-benchmark

lorikeet

Digital spoligotyping of MTB strains from Illumina read data

macaw

Macaw is a tool to lineage-type MTB samples and to identified strain mixes in WGS data sets.

nanopore-cenpk113-7d

Supplementary data for our CENPK113-7D assembly paper

ono

Order and orient

parakeet

IS6110 discovery from NGS data

parrot

Universal genotyping for Mycobacterium tuberculosis strains from WGS

peacock

peacock is a visualization library for generating vector graphics from (very) large phylogenies and many types of meta-data