We develop omics software!

 

Visit our GitHub page.
 
• 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/smangul1/seeing.beyond.target/wiki

• ImReP - a computational method for rapid and accurate pro ling of the adaptive immune repertoire from bulk RNA-Seq data
https://github.com/mandricigor/imrep/wiki

• 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/wiki

• Needle - a method for comprehensive virome, mycobiome, and eukaryome profiling on the strain level. Needle combines alignment and assembly strategies
https://github.com/smangul1/needle/wiki

• 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. Tool is 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/