I used trimmomatic to trim adapters and low quality and short reads. However, trimmomatic failed to remove the nextera-transposase adapters.
While Trim-Galore succeeded to remove these adapters, but I am still facing tow problems
Low [Per base sequence content]
Low [Sequence Duplication Levels]
Median [Sequence Duplication Levels]
Can I continue with this quality to assembly step!!!
If not, how can I improve the quality of my reads, without losing possible good reads!!