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 |