Pinned repositories

  1. 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 4

  2. atk

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

    Java 1

  3. peacock

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

    Scala 1

  4. javaml

    Java Machine Learning Library

    Java 9 7

  5. 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 …

    Java 1

  6. nanopore-cenpk113-7d

    Supplementary data for our CENPK113-7D assembly paper

  • Scala 1 GPL-3.0 Updated Aug 19, 2018
  • 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 4 GPL-3.0 Updated Jul 19, 2018
  • Java 1 Updated Jul 19, 2018
  • Java 3 1 GPL-3.0 Updated Jul 16, 2018
  • High-throughput *NA sequencing quality control

    Java 1 GPL-3.0 Updated Jul 13, 2018
  • Graph genome browser

    Java 1 GPL-3.0 Updated Jul 4, 2018
  • Digital spoligotyping of MTB strains from Illumina read data

    Scala 1 GPL-3.0 Updated Jun 18, 2018
  • Abeel Toolkit is set of utility classes that are used in our other projects.

    Java 1 Updated Apr 19, 2018
  • 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 Updated Apr 18, 2018
  • Macaw is a tool to lineage-type MTB samples and to identified strain mixes in WGS data sets.

    Scala 1 Updated Feb 28, 2018
  • Scala Updated Feb 28, 2018
  • A tool to generate synthetic aneuploid and polyploid genomes

    Python 1 MIT Updated Feb 21, 2018
  • peacock is a visualization library for generating vector graphics from (very) large phylogenies and many types of meta-data

    Scala 1 Updated Jan 17, 2018
  • Approximate tree building with kmers

    Java Updated Nov 29, 2017
  • Supplementary data for our CENPK113-7D assembly paper

    Updated Nov 20, 2017
  • Haplotype-aware de novo genome assembly for polyploid organisms from long read data

    Python 3 MIT Updated Oct 4, 2017
  • quetzal-old Archived

    Multi-reference genome browser

    Java Updated Sep 4, 2017
  • Snakemake pipeline for the PHASM genome assembler

    Jupyter Notebook 1 MIT Updated Aug 23, 2017
  • 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 1 Updated May 8, 2017
  • Java Machine Learning Library

    Java 9 7 Updated Jan 12, 2017
  • Updated Dec 15, 2016
  • Java 1 Updated Sep 28, 2016
  • Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

    Python 40 MIT Updated Sep 12, 2016
  • Jupyter Notebook 1 Updated Sep 3, 2016
  • IS6110 discovery from NGS data

    Scala GPL-3.0 Updated Jun 17, 2016
  • Order and orient

    C 1 Updated Apr 13, 2016
  • Rapid TB drug resistance determination from NGS data

    Perl GPL-3.0 Updated Mar 17, 2016
  • Emu is a tool that canonicalizes non-identical representations of large insertions and deletions (indels) and substitutions across multiple genome samples.

    Scala Updated Feb 5, 2016
  • Pilon is an automated genome assembly improvement and variant detection tool

    Scala 26 Updated Jun 25, 2015