Removing reads with repeats

[k_a_r_o_l]

Hello,

Can anyone help me. In my data I have reads like:

CACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACCCAC

ACACACACACACACACAC

CACACACACACACAC


They are in different versions and lenght.

How can I eliminate them? Any sostware, command?

[GenoMax]

What is the data format, fastq or fasta?

[k_a_r_o_l]

fastq files

[GenoMax]

You can use bbduk.sh from BBMap suite. Use "literal=CACACACACACA k=7" in addition to input output options.

Let me know if you need more help.

[k_a_r_o_l]

Thx. for help

Finally I used SGA preprocess with --dust option and I think it helped.