The Kmer Content module will do a generic analysis of all of the Kmers in your library to find those which do not have even coverage through the length of your reads. This can find a number of different sources of bias in the library which can include the presence of read-through adapter sequences building up on the end of your sequences.
You can however find that the presence of any overrepresented sequences in your library (such as adapter dimers) will cause the Kmer plot to be dominated by the Kmers these sequences contain, and that it's not always easy to see if there are other biases present in which you might be interested.
One obvious class of sequences which you might want to analyse are adapter sequences. It is useful to know if your library contains a significant amount of adapter in order to be able to assess whether you need to adapter trim or not. Although the Kmer analysis can theoretically spot this kind of contamination it isn't always clear. This module therefore does a specific search for a set of separately defined Kmers and will give you a view of the total proportion of your library which contain these Kmers. A results trace will always be generated for all of the sequences present in the adapter config file so you can see the adapter content of your library, even if it's low.
The plot itself shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.
In addition to classic adapter sequences the default configuration also includes polyA and polyG as sequences to search for. PolyA can be useful to include when looking at RNA-Seq libraries. PolyG is present as a technical artefact in 2-colour illumina libraries where it is produced when the signal from the cluster disappears. Both of these sequences are generally trimmed from the 3' end of sequences, and are therefore removed in a similar way to adapters, hence their inclusion in the default configuration. These sequences can be removed by editing the adapter_list.txt file in the Configuration directory.
This module will issue a warning if any sequence is present in more than 5% of all reads.
This module will issue a warning if any sequence is present in more than 10% of all reads.
Any library where a reasonable proportion of the insert sizes are shorter than the read length will trigger this module. This doesn't indicate a problem as such - just that the sequences will need to be adapter trimmed before proceeding with any downstream analysis.