AbeelLab

Repositories

• atk

  Abeel Toolkit is set of utility classes that are used in our other projects.
  Java 0 1 0 0 Updated May 28, 2020

• graphlift
  0 0 0 0 Updated Apr 2, 2020

• quanttb

  QuantTB is a SNP based method to identify and quantify individual strains present in tuberculosis whole genome sequencing datasets.
  Python GPL-3.0 1 1 0 0 Updated Mar 25, 2020

• ptolemy
  Scala GPL-3.0 2 8 1 0 Updated Mar 18, 2020

• cs4255

  Course material for the Algorithms for sequence-based bioinformatics course (CS4255) at TU Delft
  1 2 0 0 Updated Jan 17, 2020

• parrot

  Universal genotyping for Mycobacterium tuberculosis strains from WGS
  Scala GPL-2.0 0 0 0 0 Updated Oct 11, 2019

• 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.
  Java GPL-3.0 0 5 1 0 Updated Oct 9, 2019

• peacock

  peacock is a visualization library for generating vector graphics from (very) large phylogenies and many types of meta-data
  Scala 0 1 0 0 Updated Sep 13, 2019

• GraphClean

  Assembly graph cleaning through machine learning improves de novo long-read assembly
  Python 1 0 0 0 Updated Jun 5, 2019

• integrated_bioinformatics
  0 3 1 0 Updated Mar 11, 2019

• Alpaca

  Alpaca is a stand-alone method for identifying mosaic events in microbial genomes.
  Scala GPL-3.0 0 3 0 0 Updated Feb 12, 2019

• course_bioinformatics1819

  Course repository for Bioinformatics (NB2161) 2018-2019
  GPL-3.0 0 0 0 0 Updated Dec 6, 2018

• aneusim

  A tool to generate synthetic aneuploid and polyploid genomes
  Python MIT 1 1 0 0 Updated Oct 8, 2018

• phasm-benchmarks

  Snakemake pipeline for the PHASM genome assembler
  Jupyter Notebook MIT 0 1 0 0 Updated Sep 17, 2018

• labdocuments

  Documents supporting the lab
  0 0 0 0 Updated Sep 3, 2018

• bluejay
  Java 1 0 0 0 Updated Jul 19, 2018

• polytools
  Java GPL-3.0 1 3 0 0 Updated Jul 16, 2018

• ultraqc

  High-throughput *NA sequencing quality control
  Java GPL-3.0 0 1 0 0 Updated Jul 13, 2018

• ctag

  Graph genome browser
  Java GPL-3.0 1 0 0 0 Updated Jul 4, 2018

• lorikeet

  Digital spoligotyping of MTB strains from Illumina read data
  Scala GPL-3.0 1 1 0 0 Updated Jun 18, 2018

• prosom

  ProSOM is a promoter prediction program based on unsupervised clustering of physical properties of DNA. The program can clearly distinguish between the structural profiles of promoter sequences and other genomic sequences by using self-organizing maps.
  Java GPL-2.0 0 0 0 0 Updated Apr 18, 2018

• macaw

  Macaw is a tool to lineage-type MTB samples and to identified strain mixes in WGS data sets.
  Scala 1 0 0 0 Updated Feb 28, 2018

• hadeda
  Scala 0 0 0 0 Updated Feb 28, 2018

• kmertree

  Approximate tree building with kmers
  Java 0 0 0 0 Updated Nov 29, 2017

• nanopore-cenpk113-7d

  Supplementary data for our CENPK113-7D assembly paper
  0 0 1 0 Updated Nov 20, 2017

• phasm

  Haplotype-aware de novo genome assembly for polyploid organisms from long read data
  Python MIT 1 3 1 0 Updated Oct 4, 2017

• quetzal-old Archived

  Multi-reference genome browser
  Java 0 0 0 0 Updated Sep 4, 2017

• Pedca

  PEDCA is a ploidy estimation algorithm that infers copy number of the contigs submitted as input based on the read coverage that are aligned to them. It only requires as an input an alignment file in .bam or .sam format of a library or set of libraries aligned to a reference file of the contigs that will be estimated.
  Java 0 1 0 0 Updated May 8, 2017

• javaml

  Java Machine Learning Library
  Java 12 20 3 0 Updated Jan 12, 2017

• reports
  0 0 0 0 Updated Dec 15, 2016