tillrobin
commented
4 years ago Hello, yes one target of iMGMC was to use genome information for 16S rRNA gene sequencing. You have different options: 1: PICRUSt to get functional predictions: https://github.com/tillrobin/iMGMC/tree/master/PICRUSt , see an example application in this study: Jiang, P., Green, S.J., Chlipala, G.E. et al. Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight. Microbiome 7, 113 (2019). https://doi.org/10.1186/s40168-019-0724-4 2: You can preform close-ref picking to the reconstruced 16S rRNA sequencing and the links to the MAGs: https://github.com/tillrobin/iMGMC/blob/master/PICRUSt/iMGMC-MAGs16SrRNAlinks.tab 3: Simulation of metagenomic libraries, see our publications: Fritz, A., et al. CAMISIM: simulating metagenomes and microbial communities. Microbiome 7, 17 (2019). https://doi.org/10.1186/s40168-019-0633-6 F. Meyer, et al.: Tutorial: Assessing metagenomics software with the CAMI benchmarking toolkit bioRxiv 2020.08.11.245712; doi: https://doi.org/10.1101/2020.08.11.245712
Hope this informations are useful for you, Best Till Robin
Hi, It's really an exciting tool for the mouse gut microbiome analysis! In my study, I have obtained the 16S rRNA gene V3-V4 amplicon sequencing data of C57BL/6J mice. I'm trying to use the pre-build links between 16S rRNA genes with metagenome-assembled genomes in iMGMC. In the paper, full-length, unique 16S rRNA gene sequences were used to build the links with metagenome-assembled genomes. I'm wondering if my 16S rRNA amplicon sequencing data could also employ this tool to get the metagenome-assembled genome informations? With this pipeline Instruction to process your own WGS samples with iMGMC? Many thanks! Regards!