We develop omics software!

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Visit our <a href=”https://github.com/Mangul-Lab-USC” target=”_blank”>GitHub</a> page.

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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<br>
<a href=”https://github.com/Mangul-Lab-USC/telescope” target=”_blank”>https://github.com/Mangul-Lab-USC/telescope</a>
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• SBT – a software platform to mine discarded tumor sequences from clinical sequencing<br>
<a href=”https://github.com/smangul1/seeing.beyond.target/wiki” target=”_blank”>https://github.com/smangul1/seeing.beyond.target/wiki</a>
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• ImReP – a computational method for rapid and accurate pro
ling of the adaptive immune repertoire from bulk RNA-Seq data<br>
<a href=”https://github.com/mandricigor/imrep/wiki” target=”_blank”>https://github.com/mandricigor/imrep/wiki</a>
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• 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<br>
<a href=”https://github.com/smangul1/rop/wiki” target=”_blank”>https://github.com/smangul1/rop/wiki</a>
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• Needle – a method for comprehensive virome, mycobiome, and eukaryome profiling on the strain level. Needle combines alignment and assembly strategies<br>
<a href=”https://github.com/smangul1/needle/wiki” target=”_blank”>https://github.com/smangul1/needle/wiki</a>
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• MiCoP – a method for detecting low abundance viral and fungal organisms in metagenomic sample<br>
<a href=”https://github.com/smangul1/miCoP” target=”_blank”>https://github.com/smangul1/miCoP</a>
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• 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<br>
<a href=”https://github.com/smangul1/Microbe-scope/wiki” target=”_blank”>https://github.com/smangul1/Microbe-scope/wiki</a>
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• HapIso – a computational method to reconstruct the haploid transcriptome of a diploid organism from long single molecule reads<bR>
<a href=”https://github.com/smangul1/HapIso” target=”_blank”>https://github.com/smangul1/HapIso</a>
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• UMI-Reducer – a computational protocol allowing to differentiate PCR duplicates from biological duplicates using UMIs. Tool is designed in collaboration with Prof. Kelsey Martin<br>
<a href=”https://github.com/smangul1/UMI-Reducer/wiki” target=”_blank”>https://github.com/smangul1/UMI-Reducer/wiki</a>
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• VGA – a viral population assembly from ultra-deep sequencing data<br>
<a href=”http://genetics.cs.ucla.edu/vga/” target=”_blank”>http://genetics.cs.ucla.edu/vga/</a>

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<i class=”icon-github-circled”></i>
<br>
Visit our <a href=”https://github.com/Mangul-Lab-USC” target=”_blank”>GitHub</a> page.

center

no-repeat;center top;;

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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<br>
<a href=”https://github.com/Mangul-Lab-USC/telescope” target=”_blank”>https://github.com/Mangul-Lab-USC/telescope</a>
<br>
<br>
• SBT – a software platform to mine discarded tumor sequences from clinical sequencing<br>
<a href=”https://github.com/smangul1/seeing.beyond.target/wiki” target=”_blank”>https://github.com/smangul1/seeing.beyond.target/wiki</a>
<br>
<br>
• ImReP – a computational method for rapid and accurate pro
ling of the adaptive immune repertoire from bulk RNA-Seq data<br>
<a href=”https://github.com/mandricigor/imrep/wiki” target=”_blank”>https://github.com/mandricigor/imrep/wiki</a>
<br>
<br>
• 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<br>
<a href=”https://github.com/smangul1/rop/wiki” target=”_blank”>https://github.com/smangul1/rop/wiki</a>
<br>
<br>
• Needle – a method for comprehensive virome, mycobiome, and eukaryome profiling on the strain level. Needle combines alignment and assembly strategies<br>
<a href=”https://github.com/smangul1/needle/wiki” target=”_blank”>https://github.com/smangul1/needle/wiki</a>
<br>
<br>
• MiCoP – a method for detecting low abundance viral and fungal organisms in metagenomic sample<br>
<a href=”https://github.com/smangul1/miCoP” target=”_blank”>https://github.com/smangul1/miCoP</a>
<br>
<br>
• 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<br>
<a href=”https://github.com/smangul1/Microbe-scope/wiki” target=”_blank”>https://github.com/smangul1/Microbe-scope/wiki</a>
<br>
<br>
• HapIso – a computational method to reconstruct the haploid transcriptome of a diploid organism from long single molecule reads<bR>
<a href=”https://github.com/smangul1/HapIso” target=”_blank”>https://github.com/smangul1/HapIso</a>
<br>
<br>
• UMI-Reducer – a computational protocol allowing to differentiate PCR duplicates from biological duplicates using UMIs. Tool is designed in collaboration with Prof. Kelsey Martin<br>
<a href=”https://github.com/smangul1/UMI-Reducer/wiki” target=”_blank”>https://github.com/smangul1/UMI-Reducer/wiki</a>
<br>
<br>
• VGA – a viral population assembly from ultra-deep sequencing data<br>
<a href=”http://genetics.cs.ucla.edu/vga/” target=”_blank”>http://genetics.cs.ucla.edu/vga/</a>

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