Which computational tool should I use to remove eukaryotic sequences from my sample (created with RNA-seq and Shotgun Metagenomics and Illumina)?

Question

[BioNtE]

I have large shotgun metagenomics assembled sample. Produced by RNA-Seq and assembled with Trinity software. I would like to put it in MG-RAST to study its taxonomic composition. As MG-RAST doesn't work well with eukaryotic sequences, which computational tool can I use in order to remove them from my assembled fasta sample before putting them through MG-RAST?

Answer 1

[csidhu]

You can use EukRep (https://github.com/patrickwest/EukRep) to remove eukaryotic sequences from your datasets.