Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to report the corresponding information.
java -jar cromwell.jar run trust4.wdl --inputs inputs.json
| Parameter | Value | Description |
|---|---|---|
fastqR1 |
File | Input file with the first mate reads. |
fastqR2 |
File | Input file with the second mate reads. |
reference |
String | Reference assembly id |
| Parameter | Value | Default | Description |
|---|---|---|---|
outputFileNamePrefix |
String | "" | Output prefix, customizable. Default is the first file's basename. |
| Parameter | Value | Default | Description |
|---|---|---|---|
runTrust4.jobMemory |
Int | 8 | Memory allocated to the task. |
runTrust4.timeout |
Int | 20 | Timeout in hours, needed to override imposed limits. |
runTrust4.threads |
Int? | None | Optional threads, default is 1 |
runTrust4.modules |
String | "mixcr/3.0.13" | Names and versions of required modules. |
| Output | Type | Description | Labels |
|---|---|---|---|
cdrReport |
File | report contains CDR1,2,3 and gene information for each consensus assemblies | vidarr_label: cdrReport |
finalContigs |
File | contigs and corresponding nucleotide weight | vidarr_label: finalContigs |
finalReport |
File | report file focusing on CDR3 and is compatible with other repertoire analysis tool such as VDJTools | vidarr_label: finalReport |
consensusAssembly |
File | fasta file for the annotation of the consensus assembly | vidarr_label: consensusAssembly |
This section lists command(s) run by trust4 workflow
- Running trust4
TRUST4 runs a single command which produces a number of outputs which should be analyzed in a downstream process
set -euo pipefail
run-trust4 -f BCRTCR.fa [--ref refIMGT.fa] [-t THREADS] -1 FASTQ_R1 -2 FASTQ_R2 -o OUTPUT_PREFIX
For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .
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