ADBS-BioinfoTools is a collection of tools and scripts developed for processing and analyzing datasets generated by the ADBS consortium. ADBS (Accelerator program for Discovery in Brain disorders using Stem cells) is a scientific venture to understand mental illness by harnessing the power of genetics, genomics and stem cell technology.
The Program is a collaborative initiative of three institutions from Bengaluru, India – the Institute for Stem Cell Science and Regenerative Medicine (inStem), the National Centre for Biological Sciences (NCBS) and the National Institute for Mental Health and Neurosciences (NIMHANS). ADBS consortium generates large-scale whole genome, exome and transcriptome sequencing data by recruiting families with history of neuropsychiatric disorders. The ADBS-BioinfoTools is a set of tools/scripts developed and being employed for analyzing these datasets.
dendrogen is a tool to perform clustering of samples based on the sharing of genetic variants among them. This tool can read thousands of VCFs (Variant call files) generated from whole genome or exome sequencing and cluster them based on the allelic sharing. A cluster dendrogram is generated that helps in visualizing cluster groups.
ViV (Venn in VCFs) is a script to find the number of common genetic variants across multiple samples. This tool can simultaneously process thousands of VCF files obtained from whole genome/exome sequencing.
MIT License
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Ravi P More ([email protected])
Husayn Ahmed P ([email protected])
Shweta Joshi ([email protected])
Mahendra Rao ([email protected])
Odity Mukherjee ([email protected])
Please cite the following article to acknowledge the use of ADBS-BioinfoTools:
Suhas Ganesh, Husayn Ahmed P, Ravi K Nadella, Ravi P More, Manasa Sheshadri, Biju Viswanath, Mahendra Rao, Sanjeev Jain, The ADBS consortium, Odity Mukherjee. 2018. Exome sequencing in families with severe mental illness identifies novel and rare variants in genes implicated in Mendelian neuropsychiatric syndromes. Psychiatry and Clinical Neurosciences. doi: 10.1111/pcn.12788
Mitradas M. Panicker, Upinder S. Bhalla, and Padinjat Raghu, National Centre for Biological Sciences – Tata Institute of Fundamental Research (NCBS – TIFR), Bengaluru, India.
Odity Mukherjee, Sumantra Chattarji, and Mahendra Rao, Institute for Stem Cell Biology and Regenerative Medicine (InStem), Bengaluru, India.
Biju Viswanath, Naren P. Rao, Janardhanan C. Narayanaswamy, Palanimuthu T. Sivakumar, Arun Kandaswamy, Muralidharan Kesavan, Urvakhsh Meherwan Mehta, Ganesan Venkatasubramanian, John P. John, Meera Purushottam, Ramakrishnan Kannan, Bhupesh Mehta, Thennarasu Kandavel, Binukumar B., Jitender Saini, Deepak Jayarajan, Shyamsundar A., Jagadisha Thirthalli, Prabha S. Chandra, Bangalore N. Gangadhar, Pratima Murthy, Vivek Benegal, Mathew Varghese, Janardhan Y.C. Reddy, Sanjeev Jain, Sidney Moirangthem, and K.G. Vijay Kumar, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India.