I am analyzing raw data of Illumina reads for bacterial (Wole Genome Sequencing) using tools on the galaxy website. I used trimmomatic, and trim-Galore to remove adapters and low-quality readers.
Fastqc analysis of trimmed reads gave me this report!
Per base sequence quality
Per base sequence content
Sequence Length Distribution
Sequence Duplication Levels
Previously, I faced a problem with Nexttera Transposase sequences, but it was solved by using Trim-Galore as recommended,
1- So, Please give me your evaluation! Is it ok to use this reads for assembly!, or I should improve the quality!!, and how can I improve it!
2- Also, is it enough to assemble the paired reads, or I should also process unpaired ones as well!
Thank you for your time