Hello,

would it be possible to add Fastq trim/selection functions for NGS analysis please? Examples of relevant software can be found on Galaxy under NGS: QC and manipulation.

for instance:
Trimmomatic
FASTQ Trimmer by column
FASTQ Quality Trimmer by sliding window
Select high quality segments

Hello Nikolay,

Could you please specify what feature exactly do you need?

Why FASTQ Quality Trimmer is not enough?
See also the element integrated into the Raw DNA-Seq Processing Workflow.

Module description says that Fast Quality Trimmer scans each input sequence from the end to find the first position where the quality is greater or equal to the minimum quality threshold. Then it trims the sequence to that position.

With some reads quality does not sequentially decay from one base to another and it's possible to have bad-quality nucleotide followed by good-quality one. Therefore it would be useful to have quality trimming based on an average quality of several nucleotides within a sliding window. Average quality and window size would control the stringency of trimming.

Also, Fast Quality Trimmer does not allow to remove a fixed number of nucleotides within a read (typically in the beginning) - this is useful when analyzing e.g. libraries that were prepared using custom indexes. Although thinking a bit more about this, there is probably a way around it using Cut Adapter module with custom settings.

Thanks for the detailed description!

I see your point about considering quality of a sliding window instead of quality of a single base. This mode probably indeed should be added to the FastQ Quality Trimmer element.

As for the second case - cutting of a fixed number of bases - could you please explain what is the use case of this issue? When do we need to do so?

Quote:

As for the second case - cutting of a fixed number of bases - could you please explain what is the use case of this issue? When do we need to do so?

if the library has been constructed/amplified using primers/adapters that together with standard illumina sequences carry addition elements, e.g. for custom samples bar-coding.

In such case, library amplicons may have the following structure:

5'-[illumina sequence, constant]-[custom sequence, constant]-[sequence to be aligned, variable]-[custom sequence, constant]-[illumina sequence, constant]-3'

as I have mentioned in the previous reply, it should be possible to remove [custom sequence, constant] using Cut Adapter module by specifying the corresponding custom sequence.

Trimming .fastq by length would be useful when custom sequence is either highly complex or potentially unknown, e.g. molecular barcoding by N12. Additionally, if sequencing across [custom sequence, constant] comes back with low quality or mistakes then Cut Adapter module will not recognize it.

I am happy to share python code for length-based trimming should it be possible to integrate it into UGENE, ideally under external tools within Workflow plugin.

Thanks for the explanation!


Quote:

I am happy to share python code for length-based trimming should it be possible to integrate it into UGENE, ideally under external tools within Workflow plugin.

It might be better to implement the issue in the native C++ language, but you're welcome to send us the python script  (e.g by mail).

nice