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Table 5 Comparison of IRProfiler with existing software with respect to functionality and other S/W properties

From: IRProfiler – a software toolbox for high throughput immune receptor profiling

   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