How sickle (adaptive trimming tool) work.

Question

[Mbillah]

I am trying to understand how "sickle - A windowed adaptive trimming tool for FASTQ files using quality" work. Can any explain with a example if they have worked with this tool before? Which one is best - trimmomatic or sickle? I have paired end, illumina hiseq 2000 reads.

Thank you

[Pierre Lindenbaum]

https://github.com/najoshi/sickle

Answer 1

[Pierre Lindenbaum]

https://github.com/najoshi/sickle

Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. It will also discard reads based upon the length threshold. It takes the quality values and slides a window across them whose length is 0.1 times the length of the read. If this length is less than 1, then the window is set to be equal to the length of the read. Otherwise, the window slides along the quality values until the average quality in the window rises above the threshold, at which point the algorithm determines where within the window the rise occurs and cuts the read and quality there for the 5'-end cut. Then when the average quality in the window drops below the threshold, the algorithm determines where in the window the drop occurs and cuts both the read and quality strings there for the 3'-end cut. However, if the length of the remaining sequence is less than the minimum length threshold, then the read is discarded entirely (or replaced with an "N" record). 5'-end trimming can be disabled.

[Mbillah]

I also got this article, but i didn't understand exactly, what parameters should we use & how can i select those parameters? I got only two parameters that are length and quality threshold, is there any other parameters? Did you use it before? if yes, then it will be very nice if you share your experience with an example.