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Metagenomics Course

This 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’ capacity to conduct world class scientific research in microbial genetics and boost their institution’s profile as a leading diagnostic and scientific center.
Using the most powerful software, you will gain the latest skills in metagenomic data analysis. Resources highlighted with an asterisk are a must have.
  • Web Resources – NCBI, SILVA Database,
  • Software – MOTHUR V. 1.39, R, Excel, Adobe Suite, QIIME
  • Computing environment – Linux computing using the KIBs 5DLAB Remote Cluster
  • Software add-ons for the participant  – Required – PUTTY, WinSCP. Optional – R, XMING, BioLinux, and  Java Virtual Box
  • Laptop*
This 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 training is typically one month 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.

TOPICS & ACTIVITIES
  • Software installation
  • Definition and scope of metagenomics, metagenomics state of the art, metagenomics applications
  • NGS Techniques:  Illumina sequencing, Roche 454 sequencing. Ion Torrent: Proton / PGM sequencing, PacBio sequencing, Nanopore Sequencing
  • Microbial Identification methods: 16S rRNA, 18s rRNA , ITS, and shotgun gene sequencing
  • Community  profiling: alpha diversity, beta diversity,
  • Tests of significance, p-values, Tstatistics,  and FDR values; T-test, ANOVA, Mann-Whitney, PCOA and NMDS clustering, Random Forest
  • Classification, PERMANOVA, ANOSIM, HOMOVA, AMOVA, metastats, Lefse, and PERMDISP statistics
  • Introduction to the Linux environment on a Windows machine via JVM, Remote computing using SSH and Putty
  • Mastering Linux commands
  • Introduction to MOTHUR and QIIME
  • Creation of contigs from raw reads
  • Data 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
  • Clustering reads into OTUs, Making shared file, Classification of OTUS, Making taxonomy and phylogenetic files
  • OTU Analysis – Alpha analysis: rarefaction, Beta analysis : PCOA and NMDS plots, AMOVA, HOMOVA, Spearman correlation, UniFrac weighted, Metastats, Lefse,
  • Introduction to R
  • Analysis 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
  • Putting it all Together
The course is ideal for students and researchers working in the pharma, biotech, and medical industries. The following terms and conditions apply.
  • The fee is Kshs. 85,000/ for East African residents. Non-East African students pay 850 USD.
  • Fees covers tuition, training material, and certificate only.
  • Fees are payable strictly in advance (at least 4 working days before the starting date.
  • Groups 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
  • There 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.
  • Fee 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..
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