Table 1 Feature comparison of ClonoCalc/ClonoPlot, MiXCR [3], LymAnalyzer [4], tcR [5] and VDJtools [9]
ClonoCalc/ClonoPlot | MiXCR | LymAnalyzer | tcR & VDJtools | |
|---|---|---|---|---|
GUI |
| ✕ | ✔ | ✕ |
Demultiplexing | ✔ (wraps FASTX) | ✔ | ✕ | ✕ |
Paired-end merging | ✔ | ✔ | ✕ | ✕ |
TCR/Immunoglobulins | ✔ (wraps MiXCR) | ✔ | ✔ | ✕ |
CDR3 Extraction, including error correction | ✔ (wraps MiXCR) | ✔ | ✔ | ✕ |
V, D and J gene alignment | ✔ (wraps MiXCR) | ✔ | ✔ | ✕ |
Evaluation of relative/absolute frequency of clonotypes | ✔ | ✕ | ✕ | ✔ |
Statistics (CDR3 length, VJ gene usage) | ✔ (wraps tcR) | ✕ | ✕ | ✔ |
Descriptive statistics providing means and standard deviation (CDR3 length, VJ gene usage) |
| ✕ | ✕ | ✕ |
CDR3 intersection plots, like heatmaps and | ✔ | ✕ | ✕ | ✔ |
Venn diagrams |
| ✕ | ✕ | ✕ |
Circular visualization of similarities and differences |
| ✕ | ✕ | ✕ |
Automated documentation of all analysis steps |
| ✕ | ✕ | ✕ |
