Useful helpers for #teaching #bioinformatics: Biostars forum https://www.biostars.org & Rosalind assignment evaluator http://rosalind.info/about
Posts Tagged ‘bioinformatics’
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February 8, 2015PacBio Blog: Data Release: ~54x Long-Read Coverage for PacBio-only De Novo Human Genome Assembly
August 31, 2014http://blog.pacificbiosciences.com/2014/02/data-release-54x-long-read-coverage-for.html
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We are pleased to make publicly available a new shotgun sequence dataset of long PacBio® reads from a human DNA sample. We previously released sequence data using Single Molecule, Real-Time (SMRT®) Sequencing of ~10x coverage of this sample, sufficient for
reference-based detection of structural variation. Today we expand on that release with additional data that increases the total sequencing coverage to ~54x. This long-read data has enabled the generation of the first de novohuman genome assembly from PacBio-only sequence reads. Download the 54x long-read coverage dataset.
The dataset was generated from sequencing a well-studied human cell line (CHM1htert), which is being utilized as part of a National Institutes of Health project to sequence and assemble an alternate reference genome (the “platinum genome”). This NIH project is being led by Rick Wilson from Washington University at St. Louis and Evan Eichler from the University of Washington in collaboration with investigators from the National Center for Biotechnology Information. “}}
Oncotator
August 4, 2014http://www.broadinstitute.org/oncotator
https://github.com/broadinstitute/oncotator
Useful listing of data sources, viz:
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Protein Annotations
Site-specific protein annotations from UniProt.
Druggable target data from DrugBank.
Functional impact predictions from PolyPhen-2.
Cancer Annotations
Observed cancer mutation frequency annotations from COSMIC.
Cancer gene and mutation annotations from the Cancer Gene Census. Significant amplification/deletion region annotations from Tumorscape and theTCGA Copy Number Portal.
Overlapping Oncomap mutations from the Cancer Cell Line Encyclopedia. Significantly mutated gene annotations aggregated from published MutSiganalyses. Cancer gene annotations from the Familial Cancer Database.
Human DNA Repair Gene annotations from Wood et al.
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Uses bamboo testing software
https://www.atlassian.com/software/bamboo
Pacbio MCF-7 transscriptome dataset
July 30, 2014PAWG-WGL Links for PCAWG upload status
July 4, 2014PanCancer.info has fantastic #viz of the progress & int’l effort in the Pan-#Cancer Analysis of Whole #Genomes (#PCAWG) project
DREAM mutation calling challenge
June 7, 2014Deadlines: 7/19,8/2,8/16
https://www.synapse.org/#!Synapse:syn312572
Broad Institute’s Firehose Dashboard
March 17, 2014Contains information on analysis pipelines and datasets produced from Broad’s Firehose. Access to the protected pages requires an NCI login.
BioLayout
January 4, 2014QT:{{”
BioLayout Express3D has been specifically designed for visualization, clustering, exploration and analysis of very large network graphs in two- and three-dimensional space derived primarily, but not
exclusively, from biological data.
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http://www.biolayout.org
HuRef sperm sequencing
January 4, 2014huref on Solid
January 4, 2014QT:{{”
To demonstrate the promise of personalized genome analysis, the genome of HuRef was sequenced using the Life SOLiD™ platform. Nimbus Informatics performed the analytical work for this project and has made the resulting data available here, running entirely on the Amazon Cloud.
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http://huref.nimbusinformatics.com
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