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10x Genomics
Genome & Exome

ALIGNER_CSALIGNERALIGNER_PREFLIGHTALIGNER_PREFLIGHT_LOCALATTACH_PHASINGSUMMARIZE_REPORTS_ALIGNERALIGNATTACH_BCSMARK_DUPLICATESSETUP_CHUNKSSORT_BY_POSTRIM_READS_BCSORTERBUCKET_BY_BCBUCKET_BY_QNAMESORT_BY_BC_REPORTERDETECT_MOLECULESFILTER_BARCODESREPORT_BASICREPORT_COVERAGEREPORT_LENGTH_MASSREPORT_SINGLE_PARTITION
  ALIGNER_CS

This pipeline performs barcode processing and alignment and outputs barcode-attached reads in BAM format. This outer wrapper prepares files for final output.