Current version: v0.2.0.442

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTsQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models.

Hi-C experiments generate genomic interaction between loci located in the same or in different chromosomes. TADbit is built around the concept of a chromosome, and uses it as a central item to store and compare different Hi-C experiments. The library has been designed to be used by researchers with no expertise in computer science. All-in-one scripts provided in TADbit allow to run the full analysis using one single command line; advanced users may produce their own programs using TADbit as a complementary library.

Documentation

• TADbit documentation
• Summary of TADbit classes and functions

Feedback

If you have any question remaining, we would be happy to answer informally:

Docker

This minimal Dockerfile (resulting in a 3 Gb docker image) can be used to run TADbit in any computer:

FROM debian:8

ENV LANG=C.UTF-8 LC_ALL=C.UTF-8

RUN apt-get update --fix-missing && \
    apt-get install -y wget bzip2 --no-install-recommends && \
    rm -rf /var/lib/apt/lists/*

RUN echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
    wget --quiet --no-check-certificate https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh \
        -O ~/miniconda.sh && \
    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
    rm ~/miniconda.sh

ENV PATH /opt/conda/bin:$PATH

RUN conda config --add channels salilab && conda config --add channels bioconda && \
    conda install -y -q imp scipy matplotlib jupyter mcl samtools sra-tools pysam && \
    conda clean -y --all  && rm -rf /opt/conda/pkgs/*

RUN wget --quiet --no-check-certificate https://newcontinuum.dl.sourceforge.net/project/gemlibrary/gem-library/Binary%20pre-release%202/GEM-binaries-Linux-x86_64-core_i3-20121106-022124.tbz2 \
        -O GEM.tbz2 && \
    tar xvf GEM.tbz2 && cd GEM-*/ && \
    mv * /usr/local/bin/ && cd .. && rm -rf GEM*

RUN apt-get update --fix-missing && \
    apt-get install -y unzip build-essential --no-install-recommends && \
    wget --quiet --no-check-certificate https://github.com/fransua/TADbit/archive/dev.zip && unzip dev.zip && \
    cd TADbit-dev && python setup.py install && cd .. && rm -rf TADbit-dev dev.zip && \
    apt-get remove -y --purge unzip build-essential && \
    apt-get autoremove -y && \
    apt-get autoclean -y && \
    rm -rf /var/lib/apt/lists/*

CMD [ "/bin/bash" ]

Build the image by saving this file as Dockerfile into an empty folder and build the image from inside this empty folder with docker build -t tadbit . (~20 minutes)

Once built, run it as docker run tadbit tadbit map -h

This image contains all dependencies for TADbit and also jupyter.

To run a notebook from inside the docker container run tadbit docker image as:

docker run -it -p 8888:8888 -v /LOCAL_PATH:/mnt tadbit

LOCAL_PATH would be for example a local folder with data (e.g. FASTQs or reference genomes). And /mnt a directory inside the Docker container where the LOCAL_PATH would be mounted.

From inside docker run:

jupyter notebook --ip 0.0.0.0 --allow-root --NotebookApp.token=''

And finally write the url http://localhost:8888 in your browser.

Note: this can also be done in a single line and running in the background:

docker run -d -p 8888:8888 -v /LOCAL_PATH:/mnt tadbit jupyter notebook --ip 0.0.0.0 --allow-root --NotebookApp.token='' > /dev/null &

Citation

Please, cite this article if you use TADbit.

Serra, F., Baù, D., Goodstadt, M., Castillo, D. Filion, G., & Marti-Renom, M.A. (2017). Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors. PLOS Comp Bio 13(7) e1005665. doi:10.1371/journal.pcbi.1005665

Methods implemented in TADbit

In addition to the general citation for the TADbit library, please cite these articles if you used TADbit for:

• Mapping and read filtering [Imakaev2012] [Ay2015]
• Hi-C normalization [Imakaev2012] [Rao2014]
• A/B compartment calling [Lieberman-Aiden2009]
• Model assessemnt [Trussart2015]
• Chromatin 3D Model Building [BaùMarti-Renom2012]

Applications

TADbit has been previously used for modeling genomes and genomic domains. Here is the list of published articles:

• Alpha-globin domain [Baù2011]
• Caulobacter crescentus genome [Umbarger2011]
• TADs as regulons [Le_Dily2014]
• Yeast chromosome III [Belton2015]
• Mycoplasma pneumoniae genome [Trussart2017]

TADbit training

Next editions

• To be announced.

Past editions

• April 10th to April 11th 2017: MuG workshop: Multi-scale study of 3D Chromatin structure at the European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, (United Kingdom)
• April 3rd to April 7th 2017: Chromosomal Conformation course at the CRG training programme Barcelona (Spain)
• October 10th to October 14th 2016: 3DAROC16 3C-based data analysis and 3D reconstruction of chromatin folding at the GTPB training programme Oeiras (Portugal)
• September 28th to October 2nd 2015: Chromosomal Conformation course at the CRG training programme Barcelona (Spain)
• November 25th to November 28th 2014: CSDM 2014 at the GTPB training programme Oeiras (Portugal)
• September 6th 2014: TADbit: Automated Analysis and Three-Dimensional Modeling of Genomic Domains at ECCB14 Strasbourg (France)
• November 27th to November 29th 2013: CSDM 2013 at the GTPB training programme Oeiras (Portugal)

Bibliography

[Ay2015]

Ay, F., Vu, T.H., Zeitz, M.J., Varoquaux, N., Carette, J.E., Vert, J.-P., Hoffman, A.R. and Noble, W.S. 2015. Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C. BMC Genomics 16, p. 121.

[BaùMarti-Renom2012]

Baù, D. and Marti-Renom, M.A. 2012. Genome structure determination via 3C-based data integration by the Integrative Modeling Platform. Methods 58(3), pp. 300–306.

[Baù2011]

Baù, D., Sanyal, A., Lajoie, B.R., Capriotti, E., Byron, M., Lawrence, J.B., Dekker, J. and Marti-Renom, M.A. 2011. The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nature Structural & Molecular Biology 18(1), pp. 107–114.

[Belton2015]

Belton, J.-M., Lajoie, B.R., Audibert, S., Cantaloube, S., Lassadi, I., Goiffon, I., Baù, D., Marti-Renom, M.A., Bystricky, K. and Dekker, J. 2015. The conformation of yeast chromosome III is mating type dependent and controlled by the recombination enhancer. Cell reports 13(9), pp. 1855–1867.

[Imakaev2012]

(1, 2) Imakaev, M., Fudenberg, G., McCord, R.P., Naumova, N., Goloborodko, A., Lajoie, B.R., Dekker, J. and Mirny, L.A. 2012. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nature Methods 9(10), pp. 999–1003.

[Le_Dily2014]

Le Dily, F., Baù, D., Pohl, A., Vicent, G.P., Serra, F., Soronellas, D., Castellano, G., Wright, R.H.G., Ballare, C., Filion, G., Marti-Renom, M.A. and Beato, M. 2014. Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation. Genes & Development 28(19), pp. 2151–2162.

[Lieberman-Aiden2009]

Lieberman-Aiden, E., van Berkum, N.L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., Dorschner, M.O., Sandstrom, R., Bernstein, B., Bender, M.A., Groudine, M., Gnirke, A., Stamatoyannopoulos, J., Mirny, L.A., Lander, E.S. and Dekker, J. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950), pp. 289–293.

[Rao2014]

Rao, S.S.P., Huntley, M.H., Durand, N.C., Stamenova, E.K., Bochkov, I.D., Robinson, J.T., Sanborn, A.L., Machol, I., Omer, A.D., Lander, E.S. and Aiden, E.L. 2014. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159(7), pp. 1665–1680.

[Trussart2015]

Trussart, M., Serra, F., Baù, D., Junier, I., Serrano, L. and Marti-Renom, M.A. 2015. Assessing the limits of restraint-based 3D modeling of genomes and genomic domains. Nucleic Acids Research 43(7), pp. 3465–3477.

[Trussart2017]

Trussart, M., Yus, E., Martinez, S., Baù, D., Tahara, Y.O., Pengo, T., Widjaja, M., Kretschmer, S., Swoger, J., Djordjevic, S., Turnbull, L., Whitchurch, C., Miyata, M., Marti-Renom, M.A., Lluch-Senar, M. and Serrano, L. 2017. Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae. Nature Communications 8, p. 14665.

[Umbarger2011]

Umbarger, M.A., Toro, E., Wright, M.A., Porreca, G.J., Baù, D., Hong, S.-H., Fero, M.J., Zhu, L.J., Marti-Renom, M.A., McAdams, H.H., Shapiro, L., Dekker, J. and Church, G.M. 2011. The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Molecular Cell 44(2), pp. 252–264.