Which computational tool should I use to remove eukaryotic sequences from my sample (created with RNA-seq and Shotgun Metagenomics and Illumina)?
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?
1 answer
You can use EukRep (https://github.com/patrickwest/EukRep) to remove eukaryotic sequences from your datasets.
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