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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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Developments in sequencing technologies and methodologies have transformed the field of epigenetics, giving researchers a better way to understand the complex world of gene regulation and heritable modifications. This article explores some of the diverse sequencing methods employed in the study of epigenetics, ranging from classic techniques to cutting-edge innovations while providing a brief overview of their processes, applications, and advances.
Methylation Detect...05-31-2023, 10:46 AM -
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
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