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Assembly II: Varying the parameters

Objectives

All work for this exercise will occur in the 3.assembly/ directory.

Examining the effect of changing assembly parameters

For this exercise, there is no real structure. Make a few copies of your initial slurm scripts and tweak a few of the assembly parameters. Make sure to also change the assembly output file (e.g. from spades_assembly to spades_assembly_var1). We will compare the effects of these changes in the next lesson.

SPAdes parameters

Make a few copies of your SPAdes slurm script like so;

code

cp spades_assembly.sl spades_assembly_var1.sl

Change a few of the parameters for run time. Some potential options include

  1. Change the k-mer sizes to either a different specification, or change to the auto option
  2. Disable error correction
  3. Assemble without the --meta flag
  4. Employ a coverage cut-off for assembling

IDBA-UD parameters

Make variants of your IDBA-UD assembly script and change some parameters. Some potential options include

  1. Change the minimum/maximum k-mer sizes, or the k-mer step size
  2. Change the alignment similarity parameter
  3. Adjust the prefix length for the k-mer sub-table

Submit two or three jobs per variation.

Outputs per variant job

For all variations of your assemblies, please remember to modify -o argument from -o spades_assembly/ and -o idbaud_assembly/ in your slurm scripts to another name (e.g. -o spades_assembly_var_kmer/)