DIAMOND+LCA
DIAMOND (version 0.3.9) was run using the following command:
diamond blastx –db /ifs/mirror/diamond/nr –query <input.fastq> -v 2 –threads 16 -o <diamond.output.tsv>
LCA mapper (from mtools, MEGAN5) was run using:
lcamapper.sh -i <diamond.output.tsv> -f Detect -ms 50 -me 0.01 -tp 50 -gt megan/gi_taxid_prot.bin -o <lca.output>

https://nickilottmetagenomics.wordpress.com/2015/01/19/comparing-diamond-lca-against-kraken/

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