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@AbeelLab

AbeelLab

Pinned repositories

  1. 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 5

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

    Java 1

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

    Scala 1

  4. Java Machine Learning Library

    Java 20 12

  5. 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 …

    Java 1

  6. Supplementary data for our CENPK113-7D assembly paper

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
  • 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
  • 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
  • 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
  • Java 1 0 0 0 Updated Jul 19, 2018
  • 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
  • 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
  • 0 0 0 0 Updated Dec 15, 2016

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