Trimmed or Untrimmed reads?

[vappiah]

Dear developers,

I would like to identify contamination in my Salmonella genomes. What is the acceptable way to run? Before or after trimming of the raw paired reads.

[adamkoziol]

Hi Vincent,

We don't trim reads before processing with ConFindr. As part of its workflow, ConFindr, by default, requires the quality score of a base to be 20 in order to be counted. However, if you have particularly low quality reads and/or high sequencing depth, you might find that trimming reduces the number of false positive calls.

Best, A

[vappiah]

Thanks @adamkoziol