Passed FastQC - but adapters still present?

[tracyleighking]

Hi there - I am brand new to both Bioinformatics and this forum so I hope I'm posting in the right place; and that my questions make sense!

I have Enterococcus isolates that were sequenced using a MiSeq sequencer, and currently I've been playing around with the raw fastq files in UGENE, CGE tools, and most recently the NCBI Prokaryotic Annotation Pipeline. My aim is to check out the resistance genes, sequence types, phylogeny etc of the isolates.

I used FASTQC to check the quality of one of my isolates, then the SPAdes assembler on CGE. I then submitted to NCBI PGAP. I got an error message back though saying contam - i.e. an adapter.

I'm not sure how to proceed. I know there are (tons of) adapter trimming programs - my issue is I'm exclusively Windows based at the moment - I'm really trying to learn Unix/command line but I'm struggling with this.

Anyone have any tips; either re Windows/web based adapter trimming and/or (easy!) command line software?

Thanks so much!

[GenoMax]

You can use bbduk from BBMap suite to remove adapter contamination. BBMap suite is pure java so it will work on windows as well.