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I hope to obtain some MAGs for certain bacteria from my samples. We know they do exit in the samples by 16S amplicon, but the abundance is low. Is there any recommendation about how to assembly the MAGs for these bacteria? For instance, what software to use for binning (metabat2, maxbin2, or others), and if consensus best-quality bins shall be generated. Thank you!
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Hello hugomarquez some tools I've been familiar with are MetaBAT2, MaxBin2, CONCOCT, and MyCC. I know there are also some more recent ones I'm forgetting about but I'll try to see if I have notes stored somewhere on them in my giant list of papers to read.
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Differential Expression and Data Visualization: Recommended Tools for Next-Level Sequencing Analysis
After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, we’re wrapping up with a discussion about tools for differential gene expression analysis and data visualization. In this article, we include recommendations from the following experts: Dr. Mark Ziemann, Senior Lecturer in Biotechnology and Bioinformatics, Deakin University; Dr. Medhat Mahmoud Postdoctoral Research Fellow at Baylor College of Medicine;...05-23-2023, 12:26 PM -
Continuing from our previous article, we share variant analysis and genome assembly tools recommended by our experts Dr. Medhat Mahmoud, Postdoctoral Research Fellow at Baylor College of Medicine, and Dr. Ming "Tommy" Tang, Director of Computational Biology at Immunitas and author of From Cell Line to Command Line.
Variant detection and analysis tools
Mahmoud classifies variant detection work into two main groups: short variants (<50...05-19-2023, 10:03 AM -
With new tools and computational resources being released regularly, it can be hard to determine which are best suited for the analysis process and which older tools continue to be maintained. In an effort to assist the sequencing community, we interviewed three highly skilled bioinformaticians about their recommended tools for several important analysis applications.
Quality control and preprocessing tools
“Garbage in, garbage out” is a popular...05-16-2023, 10:11 AM
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