Skip to content


Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?


Failed to load latest commit information.
Latest commit message
Commit time
July 25, 2016 18:38
February 25, 2019 22:21
October 22, 2020 16:29
February 25, 2019 20:34
February 25, 2019 22:21
July 22, 2017 00:30
July 22, 2017 00:30
February 26, 2019 12:39
July 15, 2016 13:21
February 25, 2019 20:34
February 25, 2019 20:13
July 22, 2017 00:30
September 20, 2022 15:24

BlobTools v1.1

A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

Obtaining BlobTools

  • Option A: Download latest release
  • Option B: Clone repository
    git clone

Entering directory

cd blobtools

Install dependencies

  • Option A: Create Conda environment

    conda create -n blobtools
    conda activate blobtools
    conda install -c anaconda matplotlib docopt tqdm wget pyyaml git
    conda install -c bioconda pysam --update-deps

    Tip: Check if samtools exists by executing the command 'samtools' in the commandline. If samtools complains about dependencies, simply run the pysam install twice.

  • Option B: Install dependencies via PIP

    python install --user

Download NCBI taxdump and create nodesdb

wget -P data/
tar zxf data/taxdump.tar.gz -C data/ nodes.dmp names.dmp
./blobtools nodesdb --nodes data/nodes.dmp --names data/names.dmp

Create blobplot

./blobtools create -i example/assembly.fna -b example/mapping_1.sorted.bam -t example/blast.out -o example/test && \
./blobtools view -i example/test.blobDB.json && \
./blobtools plot -i example/test.blobDB.json


    ./blobtools --help


A docker container can be build using the following command:

     docker build -t drl/blobtools .

This docker image can be run with sample data as follows:

     docker run -v $PWD/example:/example/  -t  drl/blobtools ./blobtools create -i /example/assembly.fna -b /example/mapping_1.sorted.bam -t /example/blast.out -o /example/test