Table 5.
Comparison of IRProfiler with existing software with respect to functionality and other S/W properties
| IMGT | IGGalaxy | tcR | IMonitor | IMSEQ | IMEX | Vidjil | IRProfiler | ||
|---|---|---|---|---|---|---|---|---|---|
| Properties | S/W Interface | Graphical | Graphical | Command-line | Command-line | Command-line | Graphical | Graphical | Graphical |
| S/W Type | Web-based (Asynchronous) | Web based (Galaxy) | Native (R package) | Native (Shell script) | Native (Shell script) | Native (C# executable) | Web-based | Web based (Galaxy) | |
| TR/BcR | +/+ | −/+ | +/− | +/+ | +/+ | +/+ | +/+ | +/+ | |
| Output Files | Hundreds of files (HTML, PDF, PNG) | Tab delimited text and HTML files | R dataframes (can be saved to text) | Several PDF files | 1 Tabular text file (optionally PDF graph) | Tabular text and image files | Various files (HTML, JSON, CSV, PDF, FASTA) | Tabular text files (2 or 3 per tool) | |
| Clonotype Definition(s) | IMGT Clonotype (AA) | V + CDR3 (AA); V + CDR3 (NT); V + J + CDR3 (NT); V + D + J + CDR3 (NT) | IMGT Clonotype (AA) – works also with “relaxed” definitions | CDR3 (AA); CDR3 (NT) | V + J + CDR3 (AA) | CDR3 (AA); CDR3 (NT); V + D + J (incl. allele); whole read (NT | AA) | V(D)J junction (NT) – also supports 3rd S/W definitions | 5 definitions (see Table 2) | |
| Functionalities | Data Filtering | Conserved anchors; V/J functional; ORF | Productive reads | User-specified filtering supported | Pseudogenes; out-of-frame; stop codons; etc. | Conserved anchors; out-of-frame; stop-codons | IMGT “no result” | Conserved anchors | 11 read quality criteria |
| Clonotype Extraction | Clonotype diversity and expression | Clonotype diversity | Clonotype diversity and expression | Clonotype diversity and expression | Clonotype diversity and expression | Clonotype diversity and expression | Clonotype diversity and expression | Clonotype diversity and expression | |
| Gene Usage Calculation | V, D and J gene subgroups | V, D and J gene subgroups | V and J gene subgroups | V and J gene subgroups | N/A | V, D and J gene subgroups | N/A | V and J gene subgroups | |
| Clonotypes Comparison | Public clonotypes and number of exclusive ones | N/A | Public clonotypes | N/A | Top 10 public clonotypes | Top N (user defined) public clonotypes | Public clonotypes | Public and exclusive clonotypes | |
| Gene Usage Comparison | V, D and J gene subgroups | V, D and J gene subgroups | Entire V and J gene usage repertoire comparison | N/A | N/A | N/A | N/A | V and J gene subgroups | |
| Others | Various diversity and expression histograms (e.g., per CDR3 length), etc. | V-D, V-J and D-J gene combination heatmaps | Advanced statistics for diversity and gene usage, visualizations, etc. | Receptor annotation, error correction, visualizations | Clonotype clustering (for ambiguity resolution) | V-J gene combination heatmaps, primer efficiency analysis | Receptor annotation, Interactive visualization | N/A |