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NGS Data Analysis Course

NGS Data Analysis Course is a hands-on training designed to equip participants with knowledge and skills on how to generate, manipulate, and analyze whole genome, whole exome, and targeted NGS data. This course equips participants with skills on how to discover germline SNPs, indels, SVs, and CNVs; somatic SNVs, SVs, and indels, and RNASeq SNPs and indels. The objective is to enhance the researchers’ capacity to conduct world class scientific research and boost their institution’s profile as a leading diagnostic and scientific center.

At the end of the course, the participant will be able to:
  • Learn the science, methods and applications of Next Generation Sequencing (NGS)
  • Discover single nucleotide polymorphisms (SNPs), indels, copy number variants (CNVs), structural variants (SVs), and single nucleotide variants (SNVs) from raw sequences
  • Identify variants of clinical significance
  • Optimize therapy and diagnosis and improve clinical decisioning based on the discovered variants
Using the most powerful software, you will gain the latest skills in NGS data analysis.
  • Web Resources – NCBI Tools, HapMap, PLINK, SKAT-O, Broad Institute Resource Bundle
  • Software – SRA Toolkit, BBMAP, Fastqc, BWA, GATK, Samtools, Picard, IGV
  • High performance computing cluster – KENCLUST
  • Datasets – SRA Datasets, 1,000 Genomes Project, The Cancer Genome Atlas (TCGA)


  • NestGen Sequencing (NGS) principles, methods and technologies
  • NGS in Clinical Practice: Applications, Challenges and Promises
  • Introduction to the Linux OS and basic commands
  • SSH, Telnet, FTP, WinSCP, Putty, XMING, port forwarding and remote access
  • Accessing KENCLUST Remotely
  • Datasets and File Formats – WGET command, and SRA Tools. Fasta, Fastq, SAM and BAM file formats
  • Human reference genome (hg18, hg19, hg38), indexing the reference genome
  • NGS Data QC – Viewing reads, rimming ends, adapter removal, contaminant filtering, Kmer masking, batch processing, sequence directory
  • Read Alignment – BWA commands, PE reads in interleaved and paired files, SE reads alignment, Alignment of short and long genomes, SAI to SAM to BAM, sorting and indexing SAM files, duplicate marking, local realignment, base quality score recalibration (BQSR)
  • Variant calling and annotation – HaplotypeCaller, Unified Genotyper, SNP and Indels annotation
  • RNASEQ & Somatic SNPs, Indels and SNVs
  • Germline and somatic CNVs and SVs
This training is ideal for people in biological, medical, pharma, and biotechnology industries who wish to gain skills on how to detect genetic variations associated with disease from raw sequenced data.
  • 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 deposit, 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#NGSDA. Contact us for online payments..
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