Hello all,

I'm new to genomics and I have to assembly de novo a transcriptom (there is no reference genome yet). However it turns out that there is some contamination in the reads.

What is the best way to deal with that ?

I've checked some tools like megan, clams, deconseq but I am a bit lost in the literature and the different tools !

To me it is either possible :

1) to blastn a fraction my reads in comparison to the transcritom of some supposed other organisms and only use for assembly the reads that don't match these contaminants.

2) to assemble my reads then compare my contigs to database of other organisms. Mapping my reads to the filtered transcritom and doing re ass.

Option 1 looks easier to me

Thanks for your help !