nickp60 / blobtools

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

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