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10x Genomics
Single Cell Immune Profiling

SC_VDJ_ASSEMBLER_CSSC_VDJ_ASSEMBLERANNOTATE_CONTIGSASSEMBLE_CONSENSUSASSEMBLE_VDJBUCKET_FASTQ_BY_BCCHEMISTRY_DETECTORDETECT_CHEMISTRYCHUNK_READSCORRECT_BARCODESEXTRACT_READSFILTER_BARCODES_VDJFILTER_CONTIGSFILTER_UMISFILTER_VDJ_READSGROUP_CLONOTYPESGROUP_FASTQ_BY_BCREPORT_CONTIGSREPORT_CONTIG_ALIGNMENTSSETUP_CHUNKSSUMMARIZE_VDJ_READ_REPORTSSUMMARIZE_VDJ_REPORTSTRIM_READSVDJ_PREFLIGHTVDJ_PREFLIGHT_LOCALVLOUPE_PREPROCESS
  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.