Info

About

BasePlayer is developed by Riku Katainen in Aaltonen lab - Tumor Genomics Group, University of Helsinki. The software is based on its unpublished predecessor, RikuRator, which was programmed during 2009-2015 and which is utilized in many high-level publications (see bottom of the page).

Who is BasePlayer for?

BasePlayer is designed for life-science researchers and research groups without significant computing capacity or skills. The efficiency and versatility of BasePlayer make it also very useful tool for large groups with bioinformatics team and huge amount of data. Whether you are a scripting wizard or not, give it a try!

Citing us:

See the BasePlayer manuscript at Nature Protocols

License:

The software is under GNU AFFERO GENERAL PUBLIC LICENSE Version 3, 19 November 2007. Htsjdk Java package and BigWig reader are under MIT license and GNU Lesser General Public License (LGPL), respectively.

Source code

Available at BasePlayer project page on GitHub

Publications:

BasePlayer/RikuRator has been utilized at least in following publications:

• Katainen, R. et al. CTCF/cohesin-binding sites are frequently mutated in cancer. Nat. Genet. 47, 818-821 (2015).
• Makinen, N. et al. MED12, the mediator complex subunit 12 gene, is mutated at high frequency in uterine leiomyomas. Science 334, 252-255 (2011).
• Mehine, M. et al. Characterization of uterine leiomyomas by whole-genome sequencing. N. Engl. J. Med. 369, 43-53 (2013).
• Kiiski, J. I. et al. Exome sequencing identifies FANCM as a susceptibility gene for triple-negative breast cancer. Proc. Natl. Acad. Sci. U. S. A. 111, 15172-15177 (2014).
• Haapaniemi, E. M. et al. Autoimmunity, hypogammaglobulinemia, lymphoproliferation, and mycobacterial disease in patients with activating mutations in STAT3. Blood 125, 639-648 (2015).
• Pitkänen, E. et al. Frequent L1 retrotranspositions originating from TTC28 in colorectal cancer. Oncotarget 5, 853-859 (2014).
• Palmio, J. et al. Hereditary myopathy with early respiratory failure: occurrence in various populations. J. Neurol. Neurosurg. Psychiatry. 85, 345-353 (2014).
• Gylfe, A. E. et al. Identification of candidate oncogenes in human colorectal cancers with microsatellite instability. Gastroenterology 145, 540-543. e22 (2013).
• Mäkinen, N. et al. Exome Sequencing of Uterine Leiomyosarcomas Identifies Frequent Mutations in TP53, ATRX, and MED12. PLoS Genet 12, e1005850 (2016).
• Gylfe, A. E. et al. Eleven candidate susceptibility genes for common familial colorectal cancer. PLoS Genet 9, e1003876 (2013).
• Cajuso, T. et al. Exome sequencing reveals frequent inactivating mutations in ARID1A, ARID1B, ARID2 and ARID4A in microsatellite unstable colorectal cancer. International journal of cancer 135, 611-623 (2014).
• Mäkinen, N., Vahteristo, P., Bützow, R., Sjöberg, J. & Aaltonen, L. A. Exomic landscape of MED12 mutation-negative and-positive uterine leiomyomas. International Journal of Cancer 134, 1008-1012 (2014).
• Tuupanen, S. et al. Identification of 33 candidate oncogenes by screening for base-specific mutations. Br. J. Cancer 111, 1657-1662 (2014).
• Tanskanen, T. et al. Systematic search for rare variants in Finnish early-onset colorectal cancer patients. Cancer genetics 208, 35-40 (2015).
• Donner, I., Kiviluoto, T., Ristimäki, A., Aaltonen, L. A. & Vahteristo, P. Exome sequencing reveals three novel candidate predisposition genes for diffuse gastric cancer. Familial cancer 14, 241-246 (2015).
• Tanskanen, T. et al. Exome sequencing in diagnostic evaluation of colorectal cancer predisposition in young patients. Scand. J. Gastroenterol. 48, 672-678 (2013).
• Donner, I. et al. Candidate susceptibility variants for esophageal squamous cell carcinoma. Genes, Chromosomes and Cancer 56.6, 453-459 (2017).
• Kondelin, J. et al. Comprehensive evaluation of protein coding mononucleotide microsatellites in microsatellite-unstable colorectal cancer. Cancer Research 77(15) (2017).
• Pradhan, B. et al. Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing. Scientific reports 7.1, 14521 (2017).