How to remove the contaminant reads from plants sequencing

Question

[WAGNER]

Hey guys. I want to assemble the genome of a plant species native to the Brazilian cerrado, which was sequenced by Illumina's NextSeq (paired-end/short reads). However, even after quality control with the trimmomatic, the assemblers I used detected contaminants on both tapes. What software do you recommend to do this job?

[GenoMax]

the assemblers I used detected contaminants on both tapes.

What does this mean? How can an assembler detect contaminants?

Did your input material have contamination? If it did not then unless something bad happened during the library prep/sequencing there should be no contamination present.

[shelkmike]

First, Trimmomatic doesn't perform quality control. It performs trimming and quality filtering. Quality control is what tools like FastQC do.
Second, assemblers don't detect contamination. They assemble sequences. Contamination can be detected, for example, by aligning the contigs by Megablast to a database like NCBI nt.

If you mean contamination by DNA of some other species, it's easier to assemble the genome and then remove the contamination from contigs. See How can I remove contaminants from an assembled genome? .