# Best trim-galore parameters to improve the illumina high-seq reads

**URL:** <https://help.galaxyproject.org/t/best-trim-galore-parameters-to-improve-the-illumina-high-seq-reads/4076>\
**Category:** usegalaxy.org support\
**Tags:** devops-administration, workflow, development-tools, galaxy-local, usinggalaxy, devops\
**Created:** [July 10, 2020, 4:24pm UTC](https://help.galaxyproject.org/t/best-trim-galore-parameters-to-improve-the-illumina-high-seq-reads/4076 "2020-07-10T16:24:33Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Seraph](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/seraph/32/4289_2.png) [@Seraph](https://help.galaxyproject.org/u/Seraph)\
**Post date:** [July 10, 2020, 4:24pm UTC](https://help.galaxyproject.org/t/best-trim-galore-parameters-to-improve-the-illumina-high-seq-reads/4076/1 "2020-07-10T16:24:33Z")

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Hi all,

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!!