Need to think about whether we want to add a function that calculates the percentage of reads retained from Step 1c to the end of Step 3a? The total number of reads after illiminapairedend will include control samples whereas this won't, so need to think about if/how we want to do this.

[tdivoll]

• Number of reads output at end of first 3a block after bad sample and controls removed
  • alluniq.fasta - get read count from obicount - save as variable
• Output number of reads at end of step3a after PCR errors
  • date_alluniq.clean.fasta - save as variable
  • divide these numbers - percent_reads_retained_after_cleaning