zhouhufeng/Vardoop
A parallel variant calling tool on Hadoop
Internal utility modules for the BBCF
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A parallel variant calling tool on Hadoop
A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.
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
GATK Official Release Repository: contains the core MIT-licensed GATK framework, free for all uses