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• Telescope – an open-source web application that tracks the progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system
https://github.com/Mangul-Lab-USC/telescope

• SBT – a software platform to mine discarded tumor sequences from clinical sequencing
https://github.com/Mangul-Lab-USC

• ImReP – a computational method for rapid and accurate profiling of the adaptive immune repertoire from bulk RNA-Seq data
https://github.com/Mangul-Lab-USC/imrep

• ROP – a computational protocol to discover the source of all reads, which originate from complex RNA molecules, recombined B and T cell receptors and microbial communities
https://github.com/smangul1/rop/

• Needle – a method for comprehensive virome, mycobiome, and eukaryome profiling on the strain level. Needle combines alignment and assembly strategies
https://github.com/Mangul-Lab-USC/needle

• MiCoP – a method for detecting low abundance viral and fungal organisms in metagenomic sample
https://github.com/smangul1/miCoP

• Microbe-scope – a method to visualize the metagenomics data in the form of interactive coverage plots. It allows to detect false positives based on the coverage corresponding microbial genomes
https://github.com/smangul1/Microbe-scope/wiki

• HapIso – a computational method to reconstruct the haploid transcriptome of a diploid organism from long single molecule reads
https://github.com/smangul1/HapIso

• UMI-Reducer – a computational protocol allowing to differentiate PCR duplicates from biological duplicates using UMIs; designed in collaboration with Prof. Kelsey Martin
https://github.com/smangul1/UMI-Reducer/wiki

• VGA – a viral population assembly from ultra-deep sequencing data
http://genetics.cs.ucla.edu/vga