ConFindr

What does it do?

ConFindr looks for both intra-species and inter-species contamination in raw reads, which can cause misassemblies and erroneous downstream analysis. More details on ConFindr can be found on GitHub.

How do I use it?

Subject

In the Subject field, put ConFindr. Spelling counts, but case sensitivity doesn't.

Description

All you need to put in the description is a list of SEQIDs you want to detect contamination in, one per line.

Example

For an example ConFindr, see issue 12881.

Interpreting Results

When your request is complete, a file called confindr_output.zip will be uploaded. This contains two files: confindr_log.txt, and confindr_report.csv. The report file contains 5 columns:

  • Sample: The name of the sample
  • Genus: What ConFindr thinks the genus of the sample is. If ConFindr finds more than one genus, both will be listed here.
  • NumContamSNVs: How many times ConFindr found something that looked like a contaminating SNV. Anything 3 or over is enough to call a sample as contaminated.
  • NumUniqueKmers: How many unique kmers were found for the rMLST genes. If this number is over 45000, a sample is called as contaminated.
  • ContamStatus: Shown as True if ConFindr thinks a sample is contaminated, and False if the sample is thought to be clean.

The log file can mostly be ignored - if any unexpected errors come up, we may use it for debugging purposes.

How long does it take?

ConFindr will take between 1 and 2 minutes for each sample.

What can go wrong?

1) Requested SEQIDs are not available. If we can't find some of the SEQIDs that you request, you will get a warning message informing you of it.