MiXCR is a universal software for fast and accurate T- and B- cell receptor repertoire extraction. MiXCR support whole range of sequencing data sources, including specially prepared TCR/BCR libraries, RNA-Seq, WGS, single-cell, etc.
java -jar cromwell.jar run mixcr.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. |
Parameter | Value | Default | Description |
---|---|---|---|
outputFileNamePrefix |
String | "" | Output prefix, customizable. Default is the first file's basename. |
Parameter | Value | Default | Description |
---|---|---|---|
alignReads.jobMemory |
Int | 8 | Memory allocated to the task. |
alignReads.timeout |
Int | 20 | Timeout in hours, needed to override imposed limits. |
alignReads.threads |
Int? | None | Optional threads parameter |
alignReads.parameters |
String | "rna-seq" | Customize the type of the data analysis, possible values are rna-seq, kAligner2 and default |
alignReads.organism |
String | "hsa" | Organism recognized by MIXCr, hsa, mmu or rat (others possible). |
alignReads.reportFile |
String | "alignments.report" | Optionally, specify a name of a report file |
alignReads.library |
String? | None | Optional custom V D J library for customization of analysis |
alignReads.allowPartial |
String? | None | A useful parameter to allow partial alignments, set to true if needed |
alignReads.modules |
String | "mixcr/3.0.13" | Names and versions of required modules. |
assemblePartial.jobMemory |
Int | 8 | Memory allocated to the task. |
assemblePartial.timeout |
Int | 20 | Timeout in hours, needed to override imposed limits. |
assemblePartial.threads |
Int? | None | Threads param for fastqc |
assemblePartial.reportFile |
String | "rescued_allignments.report" | Optionally, specify a name of a report file |
assemblePartial.modules |
String | "mixcr/3.0.13" | Names and versions of required modules. |
extendAlignments.jobMemory |
Int | 8 | Memory allocated to this task. |
extendAlignments.timeout |
Int | 1 | Timeout, in hours, needed to override imposed limits. |
extendAlignments.modules |
String | "mixcr/3.0.13" | Names and versions of required modules. |
assemble.jobMemory |
Int | 8 | Memory allocated to this task. |
assemble.timeout |
Int | 1 | Timeout, in hours, needed to override imposed limits. |
assemble.modules |
String | "mixcr/3.0.13" | Names and versions of required modules. |
exportClones.jobMemory |
Int | 8 | Memory allocated to this task. |
exportClones.timeout |
Int | 1 | Timeout, in hours, needed to override imposed limits. |
exportClones.preset |
String? | None | Optional string specifying preset for output scope, full (default) min, fullImputed or minImpute |
exportClones.modules |
String | "mixcr/3.0.13" | Names and versions of required modules. |
Output | Type | Description |
---|---|---|
alignmentReport |
File | Reporting alignment metrics |
rescuedReport |
File | Reporting rescued alignments results |
exportedClones |
File | human-readable export of clone assembly results |
This section lists command(s) run by MIXCr workflow
- Running MIXCr
In its current implementation MIXCr workflow runs with RNAseq data as it's only type of input The same analysis may be conducted with a single wrapper command analyze shotgun but for the sake of flexibility and better control the analysis is divided into several tasks
ALIGN
java -jar mixcr.jar align -p ~{parameters} -s ~{organism} ~{"-OallowPartialAlignments=" + allowPartial} \
~{"-t " + threads} ~{"-b " + library} ~{"-r " + reportFile} FASTQ_R1 FASTQ_R2 alignments.vdjca
ASSEMBLE PARTIAL
java -jar mixcr.jar assemblePartial ~{alignments} ~{"-t " + threads} ~{"-r " + reportFile} alignments_rescued_1.vdjca
java -jar mixcr.jar assemblePartial alignments_rescued_1.vdjca ~{"-t " + threads} ~{"-r " + reportFile} alignments_rescued_2.vdjca
EXTEND
java -jar mixcr.jar extend ~{alignments_rescued} alignments_rescued_extended.vdjca
ASSEMBLE
java -jar mixcr.jar assemble ~{extendedAlignments} ~{customPrefix + "_clones.clns"}
EXPORT CLONES
java -jar mixcr.jar exportClones ~{assembledClones} -v ~{"-p " + preset} ~{customPrefix + "_clones.det.txt"}
For support, please file an issue on the Github project or send an email to [email protected] .
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