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

Enter directory

  cd blobtools

Install dependencies

Create Conda environment and install dependencies

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

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

DRL / blobtools

readme