Metagenomic Assembly Workshop

In this metagenomics workshop we will learn how to:

• Quality trim reads with sickle
• Perform assemblies with velvet
• Map back reads to assemblies with bowtie2

The workshop has the following exercises:

• Checking required software
  • Programs used in this workshop
  • Using which to locate a program
  • Check all programs in one go with which
  • (Optional excercise) Install sickle by yourself
• Quality trimming Illumina paired-end reads
  • Sickle
  • Downloading a test set
  • Running sickle on a paired end library
• Assembling reads with Velvet
  • Pick a kmer
  • velveth
  • velvetg
  • assemstats
  • Ray
  • (Optional exercise) VelvetOptimiser
• Mapping reads back to the assembly
  • Overview
  • Mapping reads with bowtie2
  • Some general statistics from the SAM/BAM file
  • Coverage information from BEDTools

At least a basic knowledge of how to work with the command line is required otherwise it will be very difficult to follow some of the examples. Have fun!