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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