BlobTools v1.1
A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
- Discussions, questions and answers: BlobTools GoogleGroup
- Issues, bug reports and feature requests: GitHub issues
- Documentation: blobtools.readme.io
- Citation: Laetsch DR and Blaxter ML, 2017
Obtaining BlobTools
- Option A: Download latest release
- Option B: Clone repository
git clone https://github.com/DRL/blobtools.git
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 setup.py install --user
Download NCBI taxdump and create nodesdb
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz -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
Usage
./blobtools --help
Docker
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