NGS Analysis Pre-conference Workshop – Genomics India 2019

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23rd Jan 2019,at Chancery Pavilion, Bengaluru
Preconference Workshop on NGS Data Analysis on 23rd January 2019
Short read, Long read and hybrid Analysis
Time Session Topics
9:00-9:30 AM Introduction to NGS technologies
  • Short reads vs Long reads
9:30–10:00 AM Data processing for short reads
  • Quality – FastQC and Q-Score
  • File format and type conversion – Fastq and Fasta
  • Removing adapters/barcodes –  Cutadapt and Trimgalore
10:00 – 10:30 AM Long read sequencing and basecalling
  • Nanopore live run
  • Basecalling – Albacore, Guppy
10:30 – 11:00 AM Tea Break
11:00 – 1:00 PM
Metagenome Analysis
  • Short reads 16s vs Long reads 16s – QIIME, EPI2ME 16S Analysis
  • Whole genome metagenome analysis -EPI2ME WIMP

Metaspades, MEGAN

1:00 – 2:00 PM Lunch
2:00 – 3:30 PM

De novo Assembly using short and long reads

  • Error Correction – Canu
  • Assembly – Canu, Spades and MaSuRCA
  • Polishing – Nanopolish, Pilon
3:30 – 4:00 PM Tea Break + discussion
4:00 – 5:30 PM

Genome Annotation

Gene prediction – Augustus

  • Functional Annotation

Comparative Analysis

  • Circos plots – Brig
  • Workshop includes – Lecture, demonstration and hands on [Join in a group]
  • Bring your own laptop for Data Analysis.