Can FermiKit be run on Amplicon data from targeted re-sequencing

[dgaston]

Hi Heng,

Always interested to test out new software that you put out. I am doing a lot of targeted resequencing with Illumina TruSight Amplicon data of tumour-only samples. I have been looking for some assembly-based methods since there are some tandem-duplications and large indels in some of our samples that are difficult to detect with standard methods. I just tested this out on one of my samples and at the end I have no variants at all. The sorted bam file doesn't appear to have anything aligned against the reference.

Just wanted to check whether in principal fermikit will work on this data before I dive too deep into debugging and trying alternate parameters from the standard defaults on the Readme.

Cheers

[lh3]

I have tried fermikit on target sequencing. The result makes certain sense, but as I am not familiar with such applications, I can say little about the accuracy. For the time being, I would not recommend to use it to target sequencing, unless you want to spend time on understanding the results.

In addition, for target sequencing, I was choosing reads consisting of Q20 bases only and skipping error correction (fermi2.pl unitig -E).