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Table 4 Comparison of functionalities offered by TRIP and the Galaxy IRProfiler tools

From: TRIP - T cell receptor/immunoglobulin profiler

Feature TRIP GALAXY IRProfiler
Data processing Multiple samples processing per session One sample per session
Data filtering Two stages of filtering: preselection and selection with filtering choices for V-Region, CDR3 and V-D-J gene One step of data filtering with same parameters. Indels are also included
Clonotype computation There are 10 different clonotype definitions from which the user might choose. Convergent evolution of each clonotype is also computed, when possible. Linking each clonotype with the sequences (and all related information) which are assigned to, is also possible. Only three clonotype definitions: V+CDR3, J+CDR3, CDR3
Highly similar computation Highly similar clonotypes merged based on user defined CDR3 thresholds Not supported
Repertoires extraction Multiple repertoire extraction for V-D-J gene (and allele). Choice of repertoire extraction based on highly similar clonotypes given Only V and J gene repertoire extraction
Repertoire comparison Comparison of V, D and J gene and allele usage among multiple repertoires Comparison of gene usage for V and J subgroups among multiple repertoires
Shared clonotypes Shared clonotypes among datasets including/excluding singletons, V-gene (based on the clonotypes definition) Shared clonotypes among datasets including/excluding singletons. In order to exclude the V gene users have to re-analyze the datasets
CDR3 distribution CDR3 distribution with output visualization plots Not supported
Pi distribution Pi distribution with output visualization plots Not supported
Multiple value comparison Multiple comparisons between V-D-J gene, molecular mass, and pI Not supported
Alignment An alignment table is computed for the selected region (V-D-J REGION, V-J REGION). A grouped alignment table is computed as well. The selected region can be aligned at nucleotide level, at amino acid level or both. The reference sequences used can be at allele level or at gene level. The user can also insert his/her own reference sequence. Not supported
Somatic hypermutations A table with the mutations based on alignment table is computed Not supported
Visualization Output bar plots, pie charts and logo graphs is supported Not supported