Dear All:
Does anyone know an efficient tool or script that removes certain reads with from Fastq file  when it matches specific sequence?
this means : if the reads contain my sequence so the entire read should be completely removed from the FASTQ file.

Many many thanks
Use [seqkit grep][1]:

    $ zcat input.fq.gz | seqkit grep -v -s -i -p aggcg

This will remove all reads containing "aggcg".


  [1]: https://bioinf.shenwei.me/seqkit/usage/#grep