profiling: kaiju
Use kaiju
for taxonomic profiling (repo).
-
conda
YAML file -
rule(s) for databases -
rule(s) for profiling -
rule(s) for summaries -
rule(s) for krona
input/plots
Input/output: ref: merge outputs
- PE and SE separately for MG/MT, i.e. 4 outputs per sample
- joint output PE+SE for MG/MT, i.e. 2 joint outputs per sample
- see also kaiju issue 9
- joint output MG+MT from PE+SE, i.e. 1 joint output per sample
Parameters: ref: accuracy
For highest sensitivity, it is recommended to use the nr database (+eukaryotes) [...]. Alternatively, use proGenomes over Refseq for increased sensitivity.
Greedy run mode yields a higher sensitivity compared with MEM mode.