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10x Genomics
Single Cell Immune Profiling

Cell Ranger , printed on 04/13/2025

SC_VDJ_ASSEMBLER_CSBUILD_VDJ_OUTPUTS_CSFULL_VDJ_INPUTSPICK_VDJ_OUTSSC_MULTI_CORECOPY_VDJ_REFERENCECOUNT_ANALYZERDISABLE_FEATURE_STAGESMAKE_FULL_CONFIG_MAKE_VDJ_CONFIGMULTI_CHEMISTRY_DETECTORCOMBINE_GEM_WELL_CHEMISTRIES_GEM_WELL_CHEMISTRY_DETECTORCHECK_BARCODES_COMPATIBILITYDETECT_COUNT_CHEMISTRYVDJ_CHEMISTRY_DETECTORCHECK_BARCODES_COMPATIBILITY_VDJDETECT_CHEMISTRYDETECT_VDJ_RECEPTORMULTI_GEM_WELL_PROCESSORCOUNT_GEM_WELL_PROCESSORVDJ_B_GEM_WELL_PROCESSORMULTI_SETUP_CHUNKSSC_VDJ_CONTIG_ASSEMBLERASSEMBLE_VDJBARCODE_CORRECTIONHANDLE_GEX_CELLSMAKE_SHARDMERGE_METRICSRUST_BRIDGEVDJ_T_GEM_WELL_PROCESSORMULTI_SETUP_CHUNKSSC_VDJ_CONTIG_ASSEMBLERASSEMBLE_VDJBARCODE_CORRECTIONHANDLE_GEX_CELLSMAKE_SHARDMERGE_METRICSRUST_BRIDGEMULTI_REPORTERBUILD_MULTI_WEB_SUMMARYCLOUPE_PREPROCESSSUMMARIZE_REPORTSVDJ_B_REPORTERREPORT_CONTIGSSUMMARIZE_VDJ_REPORTSVLOUPE_PREPROCESSWRITE_CONTIG_OUTSWRITE_CONTIG_PROTOVDJ_T_REPORTERREPORT_CONTIGSSUMMARIZE_VDJ_REPORTSVLOUPE_PREPROCESSWRITE_CONTIG_OUTSWRITE_CONTIG_PROTOSPLIT_VDJ_INPUTSVDJ_B_CLONOTYPE_ASSIGNERCLONOTYPE_ASSIGNERCREATE_AIRR_TSVFILL_CLONOTYPE_INFORUN_ENCLONEWRITE_ANN_CSVWRITE_CLONOTYPE_OUTSWRITE_CONCAT_REF_OUTSWRITE_CONSENSUS_BAMWRITE_CONSENSUS_TXTHANDLE_NO_VDJ_REFVDJ_T_CLONOTYPE_ASSIGNERCLONOTYPE_ASSIGNERCREATE_AIRR_TSVFILL_CLONOTYPE_INFORUN_ENCLONEWRITE_ANN_CSVWRITE_CLONOTYPE_OUTSWRITE_CONCAT_REF_OUTSWRITE_CONSENSUS_BAMWRITE_CONSENSUS_TXTHANDLE_NO_VDJ_REFVDJ_PREFLIGHTVDJ_PREFLIGHT_LOCAL_STRUCTIFY
←  SC_VDJ_ASSEMBLER_CS

This is the main Cell Ranger V(D)J pipeline that assembles and annotates single-cell V(D)J transcript sequences. This outer wrapper pipeline prepares files for final output.