{"id":781,"date":"2024-03-17T11:09:07","date_gmt":"2024-03-17T08:09:07","guid":{"rendered":"https:\/\/www.kibs.co.ke\/wp\/?page_id=781"},"modified":"2026-07-21T12:38:08","modified_gmt":"2026-07-21T09:38:08","slug":"metagenomics-course","status":"publish","type":"page","link":"https:\/\/www.kibs.co.ke\/research\/metagenomics-course\/","title":{"rendered":"Metagenomics Course"},"content":{"rendered":"\n\n
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\n\n\n\nThis hands-on training will equip participants with knowledge and skills on how to generate, manipulate, and analyze 16s rRNA, 18S rRNA, and ITS sequencing data. The objective is to enhance the researchers\u2019 capacity to conduct world class scientific research in microbial genetics and boost their institution\u2019s profile as a leading diagnostic and scientific center.\n\n\n\n
\"Metagenomics<\/figure>\n\n\n\n\n\n\n\nUsing the most powerful software, you will gain the latest skills in metagenomic data analysis. Resources highlighted with an asterisk are a must have.\n\n\n\n\nWeb Resources – NCBI, SILVA Database<\/a>, MGnify<\/a>, MicrobiomeAnalyst<\/a>, GOLD<\/a>\n\n\n\nSoftware – MOTHUR V. 1.46, R, Excel, Adobe Suite, QIIME\n\n\n\nComputing environment – Linux computing using the KIBs KENCLUST HPC\n\n\n\nSoftware add-ons for the participant  – Required \u2013 PUTTY, WinSCP. Optional – R, XMING, BioLinux, and  Java Virtual Box\n\n\n\nParticipants must have their own computers to work on<\/strong> and a stable internet connection for the duration of the course<\/strong>.\n\n\n\n\n\n\n\n\nThis is an 8-day intensive and hands-on training program. Training hours and days are flexible and will be customized to fit each participant’s schedule. The duration of the metagenomics course is typically 8 days but may be shorter or longer depending on each participant’s availability and commitment.  Training is mostly dry-lab based and practical hands-on with some few theoretical lessons.   Online classes can be arranged.


METAGENOMICS COURSE TOPICS & ACTIVITIES<\/strong>
\n\n\n\n\nSoftware installation\n\n\n\nDefinition and scope of metagenomics, metagenomics state of the art, metagenomics databases and applications\n\n\n\nNGS Techniques:  Illumina sequencing, Roche 454 sequencing. Ion Torrent: Proton \/ PGM sequencing, PacBio sequencing, Nanopore Sequencing\n\n\n\n\n\n\nMicrobial Identification methods: 16S rRNA, 18s rRNA , ITS, and shotgun gene sequencing\n\n\n\nCommunity  profiling: alpha diversity, beta diversity,\n\n\n\n\n\nTests of significance, p-values, Tstatistics,  and FDR values; T-test, ANOVA, Mann-Whitney, PCOA and NMDS clustering, Random Forest\n\n\n\nClassification, PERMANOVA, ANOSIM, HOMOVA, AMOVA, metastats, Lefse, and PERMDISP statistics\n\n\n\n\n\nIntroduction to the Linux environment on a Windows machine via JVM, Remote computing using SSH and Putty\n\n\n\nMastering Linux commands\n\n\n\n\n\nIntroduction to MOTHUR and QIIME\n\n\n\nCreation of contigs from raw reads\n\n\n\n\n\nData Pre-processing – Quality trimming, Deduplication of sequences , Removal of potential redundancies arising from trimmed ends ,Pre-clustering to further remove any noise , Sorting by abundance from most abundant to least abundant, Removal of chimeras using the VSEARCH algorithm, Lineage removal, Assessment of error rates using a mock community\n\n\n\nClustering reads into OTUs, Making shared file, Classification of OTUS, Making taxonomy and phylogenetic files\n\n\n\n\n\nOTU Analysis – Alpha analysis: rarefaction, Beta analysis : PCOA and NMDS plots, AMOVA, HOMOVA, Spearman correlation, UniFrac weighted, Metastats, Lefse,\n\n\n\nIntroduction to R\n\n\n\n\n\nAnalysis and Graphging using R – Stacked bar\/area plot, Interactive pie chart, Rarefaction curves, Phylogenetic tree, Heat tree analysis, FB Ratio, Chao 1 index, ACE index, Shannon index, Simpson index, Fisher index, T-test\/ANOVA p-value & T-statistic Mann-Whitney\/Kruskal-Wallis  pvalue & Mann-Whitney statistic, PCOA plot, PERMANOVA, ANOSIM, PERMDISP statistics, Results table, Heatmap image, Hierarchical Clustering & Heatmap Visualization, Tree based on unweighted Unifrac distance, SparCC correlation tables, network, and boxplots, T-test\/ANOVA p-value & T-statistic Mann-Whitney\/Kruskal-Wallis  pvalue & Mann-Whitney statistic, Zero inflated Gaussian fit: p-values and FDR values, log2FC, logCPM, P-values, and FDR values, LDA scores, p-values, FDR values, analysis results table, MDA Accuracy, OOB error rates, RF plots, important features\n\n\n\nPutting it all Together\n\n\n\n\n\n\n\nThe course is ideal for students and researchers working in the pharma, biotech, and medical industries. The following terms and conditions apply.\n\n\n\n\nThe fee is Kshs. 85,000\/ for East African residents. Non-East African students pay 850 USD.\n\n\n\nFees covers tuition, training material, and certificate only.\n\n\n\nFees are payable strictly in advance (at least 4 working days before the starting date.\n\n\n\nGroups with a minimum of 5 people will enjoy a 10% discount and early bird registration (at least 2 weeks before the start) will be offered a 5% discount\n\n\n\nThere will be a 10% administrative charge for cancellations received in writing up to 20 working days before the start of the course. No refunds will be made for cancellations received within 20 working days of the course start date or for the inability to attend the course for whatever reasons. Substitutions may, of course, be made at any time, providing you inform us in writing. KIBs is not liable for non-attendance due to travel disruptions, health problems or any other reason that might lead to a delegate not being able to attend the course.\n\n\n\nFee is payable by direct depsoit, bankers cheque or MPESA to: Bioinformatics Institute of Kenya Ltd. A\/C No. 0012342070001, Cooperative Bank of Kenya, Co-op House Branch, Nairobi, Kenya. The Paybill number for payments via Mpesa is 400222 and the account number is 1679821#your name. Contact us for online payments..\n\n\n\n\n\n\n\n\nKindly fill the form details below to register for your course of interest.
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Course Registration Form<\/h2>\n\n
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Course Information<\/h3>\n\n
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