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tested_parameters.txt
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kraken on raw reads, read threshold100 (100 filt)
unfiltered
200
500
metaspades & kraken 100_filt
unfilt
250 filt
coverage filtering: minimum coverage = 1
1.5
1.25
default coverage filter
metaphlan unfiltered
200 filt
500 filt
diamond (with metaspades) unfiltered no read threshold
unfiltered contig length 4 filt
unfiltered contig length 100 filt
unfiltered contig length 200 filt
unfiltered contig length 500 filt
minimum contig length 100 unfiltered
4 filt
100 filt
200 filt
500 filt
minimum contig length 250 unfiltered
4 filt
100 filt
200 filt
500 filt
Kaiju GREEDY mode unfiltered
100 filt
200 filt
500 filt
KAIJU MEM mode unfiltered
100 filt
200 filt
500 filt
KrakeknUniq on contigs unfiltered
3 reads 3 minimum kmers 0.0003 covergae
5 reads 5 unique kmers 0.0005 covergae
10 reads 10 unique kmers 0.001 covergae
25 reads 50 kmers 0.0025 coverage
50 reads 50 unique kmers 0.005 minimum coverage
100 reads 100 unique kmers 0.01 coverage
gottcha unfiltered
megahit assembly + Kraken (with prune=2 parmaeter)
megahit assembly + kraken (with prune=6 parameter)
megahit assembly + kraken (with prune=10 parameter)
megahit assembly + metaphlan (with prune=2)
megahit assembly + metaphlan (with prune =6)
megahit assembly + metaphlan (with prune=10)
Centrifuge unfiltered
centrifuge 100 filt
centrifuge 150 filt
centrifuge 200 filt
motus2 unfiltered at genus level
motus2 unfiltered at species level
pathseq unfiltered
pathseq >0 filtered
pathseq >1 filtered
classification intersection: motus and spades/kraken with 4 contig threshold
classification union: motus and spades/kraken with 4 contig threshold
consensus classification: single tools (pathseq, motus and kraken on contigs) + whole consensus combination
consensus kraken + motus
consensus kraken + pathseq
consensus pathseq + motus
human depletion - bbduk default parameters
bwa
bwa + bbduk
kontaminant
BBDuk parameter optimisation: mcf 0.5
MCF 0.75
mcf 0.9
MKF 0.5
MKF 0.75
MKF 0.9
MCF 0.5 with human reference + cosmic cancer database
viral classifications (various datasets either 50k reads per viral sepcies or 10k)- kraken on assembled contigs
kraken on raw reads
Pathseq on a single viral dataset to investigate how that performs