I downloaded some paired end sequencing files as a fastq format.
I would like to make sure that there are no hidden problems which might be more difficult to detect at a later state, so I ran FastQC to check their sequence quality before analyzing them.
Unfortunately, there are some bad conditions in some samples. Especially, per base sequence content and sequence duplication levels and adapter content are common bad categories I mainly encountered.
I heard that there are some tools that do removing reads that are bad or biased so I tried to search and finally found that "Trimmomatic" seemed to what I am looking for. However, after I examined their manual in detail, that is not for my case. This is because my problems is mainly focused on sequence duplication levels, per base sequence content,kmer content not a base quality or related sequence quality something.
Therefore I need to find another tools that suits for my case. but I didn't.
Can you suggest or recommend any preprocessing-related tools for me?
especially in case of resolving sequence duplication level or per base sequence content.