mixcr

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.

Dependencies

• mixcr 3.0.13
• java 8

Usage

Cromwell

java -jar cromwell.jar run mixcr.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
fastqR1	File	Input file with the first mate reads.
fastqR2	File	Input file with the second mate reads.

Optional workflow parameters:

Parameter	Value	Default	Description
outputFileNamePrefix	String	""	Output prefix, customizable. Default is the first file's basename.

Optional task parameters:

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.

Outputs

Output	Type	Description
alignmentReport	File	Reporting alignment metrics
rescuedReport	File	Reporting rescued alignments results
exportedClones	File	human-readable export of clone assembly results

Commands

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"}

Support

For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .

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