Table 1.
Total number of genes, for each method, from which one or more reads could not be classified as human (i.e. false negative calls) or to which one or more microbial reads had been misclassified (i.e. false positive calls). Note that as the current Centrifuge and Kraken RefSeq-based databases contain human assembly GRCh38, it is unnecessary to create an equivalent with GRCh37
|
Method |
No. of human genes for which one or more reads could not be classified as human, across all species and all replicates of that method (i.e. false negative classifications) |
No. of human genes to which one or more microbial reads had been misclassified, across all species and all replicates of that method (i.e. false positive classifications) |
||
|---|---|---|---|---|
|
GRCh38.p12 |
GRCh37.p13 |
GRCh38.p12 |
GRCh37.p13 |
|
|
Bowtie2 |
627 |
593 |
0 |
0 |
|
BWA-mem |
0 |
0 |
13 170 |
587 |
|
Centrifuge (human) |
23 |
n/a |
0 |
n/a |
|
Centrifuge (RefSeq) |
25 |
n/a |
0 |
n/a |
|
GEM |
42 |
64 |
120 |
110 |
|
HISAT2 |
14 943 |
14 211 |
0 |
0 |
|
Kraken2 (human) |
1547 |
n/a |
0 |
n/a |
|
Kraken2 (RefSeq) |
37 |
n/a |
0 |
n/a |
|
Novoalign |
3588 |
3367 |
11 |
10 |
|
minimap2 |
660 |
516 |
443 |
421 |
|
SMALT |
0 |
2 |
35 518 |
33 874 |
|
SNAP |
3283 |
3047 |
0 |
0 |