Description: Commercially available software for visualization and analysis of next generation. Single-Cell Genomics Microbial/Metagenomics Gene Regulation Data and Pipeline Management NGS Variant Assessment SARS-CoV-2 Solutions Discovery & Research Powerful digital insights to help you innovate, integrate and translate scientific results into impactful discoveries. Message me if you'd like to see some codes I've used or have any other questions. Proper Citation: CLC Genomics Workbench (RRID:SCR011853). The de novo assembly algorithm of CLC Genomics Workbench offers comprehensive support for a variety of data formats, including both short and long reads, and mixing of paired reads (both insert size and orientation). I would encourage you to seek further support in your research community and start fiddling around with RStudio and these various packages. I feel publishing with these types of R packages are more credible in the literature as well. I don't know where you are at in your career, but learning these tools has made me feel ahead of the game and more trusting of my results. Yes, we use CLC Genomics Workbench and their Microbial Genomics Module. Many others have stood where you're standing, resulting in a lot of blog posts etc. Although, command line analysis is quite difficult at times to learn and incredibly frustrating, it's not impossible. Therefore, I would advise to use CLC as more of a preliminary analysis tool. CLC Genomics Workbench Technical Setup Details Software Full Name: CLC Genomics Workbench Setup File Name: CLCGenomicsWorkbenchv3.6.5. I ended up getting clearer results that I trusted and understood better after abandoning CLC and using DESeq and EdgeR (with DESeq being my preferred method). Supports a very wide range of NGS bioinformatics applications. Hi Cristina, I previously used CLC for RNA-Seq analysis and fiddled with lots of parameters, my final output delivered a low number of differentially expressed genes (DEG) that were uninformative. Message me if you'd like to see some codes I've used or have any other questions. I don't know where you are at in your career, but learning these tools has made me feel ahead of the game and more trusting of my results. I ended up getting clearer results that I trusted and understood better after abandoning CLC and using DESeq and EdgeR (with DESeq being my preferred method). The mechanisms used by the parasite to support its life strategy are of great interest for developing control.
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