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 FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called 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
PythonGPL-3.0
Current version: v0.2.0.58
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 FASTQ
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.
If your question is still unanswered feel free to open a new issue.
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:
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.
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.
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.
Enright, A. J., Van Dongen, S., & Ouzounis, C. A. (2002). An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research, 30(7), 1575–1584.
[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 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-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.
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.
Russel, D., Lasker, K., Webb, B., Velázquez-Muriel, J., Tjioe, E., Schneidman-Duhovny, D., et al. (2012). Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies. PLoS Biology, 10(1), e1001244.
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.
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.
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.
