ngsCAT can be downloaded from the following link:

• Version 0.1 (20/01/2014, 1.6 MB): ngscat.v0.1.tar.gz

See detailed instructions about manual installation of ngsCAT and its dependencies in section 3.3.1 of the online documentation. For an automatic installation, see “Installation scripts” below.

UPDATE!: visit the new docker section to run ngscat in a few seconds!

With the aim of making the installation of ngsCAT and its dependencies easier, installation scripts for different Unix-based distributions are provided. These scripts automatically download and install ngsCAT source code and its dependencies (see section 3.3.2 in the online documentation). Choose proper script according to your distribution:

• Ubuntu-based distributions: setup_ubuntu.sh (tested in Linux Mint 12, 13 and 15 and Ubuntu 12.04 and 13.10).
• Debian-based distributions: setup_debian.sh (tested in Debian 7)
• Fedora-based distributions: setup_fedora.sh (tested in Fedora 20)

• A version of the online documentation in PDF format is available here. Documentation is also given together with ngsCAT source code.

The following sinthetic examples have been run with ngsCAT (see section 7 of the online documentation).

• Example 1:
  • BAM file: example1.bam (right click and save as, 106 MB)
  • BED file: seqcap.example1.bed (145 kB)
  • Reference genome: hg19.tar.gz (right click and save as, 829 MB)
  • Report generated by ngsCAT (default execution):download
  • Report generated by ngsCAT (full execution): download
• Example 2:
  • BAM file: example2.bam (right click and save as, 52 MB)
  • BED file: seqcap.example2.bed (100 kB)
  • Reference genome: the same as in example 1
  • Report generated by ngsCAT: download
• Examples 1 and 2 run at a time:
  • Report generated by ngsCAT: download

Three whole-exome experiments taken from the 1000 genomes project are run through ngsCAT (see section 8 in the online documentation):

• HG00096:
  • BAM file: hg00096.bam (right click and save as, 9.2 GB) (original link)
  • BED file: exome.targets.g1k.bed (4 MB) (original link)
  • Reference genome: hg19.wochr.tar.gz (right click and save as, 829 MB)
  • Report generated by ngsCAT: download
• HG00097:
  • BAM file: hg00097.bam (right click and save as, 5.8 GB) (original link)
  • BED file: exome.targets.g1k.bed (4 MB) (original link)
  • Reference genome: hg19.wochr.tar.gz (right click and save as, 829 MB)
  • Report generated by ngsCAT: download
• HG00099:
  • BAM file: hg00099.bam (right click and save as, 7.9 GB) (original link)
  • BED file: exome.targets.g1k.bed (4 MB) (original link)
  • Reference genome: hg19.wochr.tar.gz (right click and save as, 829 MB)
  • Report generated by ngsCAT: download

We have developed a docker image to run ngscat without any manual installation. Please visit our repository in dockerhub: https://hub.docker.com/r/clinbioinfosspa/ngscat

If you are interested in build your own docker image, have a look to the dockerfile:

FROM debian:wheezy
RUN apt-get update && apt-get -y install python zlibc zlib1g zlib1g-dev samtools python-numpy python-scipy python-xlwt python-matplotlib wget curl
RUN wget -O - https://bootstrap.pypa.io/get-pip.py -o get-pip.py|python
RUN pip install 'requests[security]' pysam==0.7.6 pybedtools==0.8.0 progressbar==2.5
WORKDIR /
RUN wget -O - http://ngscat.clinbioinfosspa.es/_media/ngscat/download/ngscat.v0.1.tar.gz | tar xzf -
RUN ln -s /ngscat.v0.1 ngscat && chmod +x /ngscat/ngscat.py
RUN echo "backend: agg" > /etc/matplotlibrc
ENTRYPOINT ["/ngscat/ngscat.py"]