Checking & Removing Index Sequences from Illumina reads

Question

[tahsin56]

I am very new to metagenomics stuff. I have some Illumina HiSeq sequencing reads. I have 1 forward fastq file and 1 reverse fastq file. I also have 2 other files which happen to be index files.

How do I check, if my raw reads have indices still present in them and if so how do I remove them from my reads?

I know it cannot be done using trimmomatic.

TIA.

Answer 1

[GenoMax]

In case of standard Illumina sequencing index reads are never a part of actual sequence of insert. If you have separate files for the indexes then that is where index sequences are.

[tahsin56]

Thanks. Yes, I have 2 separate index files for my reads. What should I do with those? Are they somehow necessary in the assembly or quality trimming? TIA.

[GenoMax]

Not sure what software you are going to use for downstream analysis but here is the workflow for Illumina for Qiime. Similar workflow for mothur is available here.