Usage: mixcr assemble [--write-alignments] [--cell-level] [--sort-by-sequence]
                      [--dont-infer-threshold] [--high-compression] [--assemble-clonotypes-by
                      <gene_features>] [--split-clones-by <gene_type>]... [--dont-split-clones-by
                      <gene_type>]... [-O <key=value>]... [-P <key=value>]... [--report <path>]
                      [--json-report <path>] [--use-local-temp] [--force-overwrite] [--no-warnings]
                      [--verbose] [--help] alignments.vdjca clones.(clns|clna)
Assemble clones.
      alignments.vdjca       Path to input file with alignments.
      clones.(clns|clna)     Path where to write assembled clones.
  -a, --write-alignments     If this option is specified, output file will be written in "Clones &
                               Alignments" format (*.clna), containing clones and all corresponding
                               alignments. This file then can be used to build wider contigs for
                               clonal sequence or extract original reads for each clone (if
                               -OsaveOriginalReads=true was use on 'align' stage).
                               Default value determined by the preset.
      --cell-level           If tags are present, do assemble pre-clones on the cell level rather
                               than on the molecular level.
                             If there are no molecular tags in the data, but cell tags are present,
                               this option will be used by default.
                             This option has no effect on the data without tags.
                               Default value determined by the preset.
  -s, --sort-by-sequence     Sort by sequence. Clones in the output file will be sorted by clonal
                               sequence,which allows to build overlaps between clonesets.
                               Default value determined by the preset.
      --dont-infer-threshold Turns off automatic inference of minRecordsPerConsensus parameter.
                               Default value determined by the preset.
      --high-compression     Use higher compression for output file.
      --assemble-clonotypes-by <gene_features>
                             Specify gene features used to assemble clonotypes. One may specify any
                               custom gene region (e.g. `FR3+CDR3`); target clonal sequence can
                               even be disjoint. Note that `assemblingFeatures` must cover CDR3
      --split-clones-by <gene_type>
                             Clones with equal clonal sequence but different gene will not be
                               merged.
      --dont-split-clones-by <gene_type>
                             Clones with equal clonal sequence but different gene will be merged
                               into single clone.
  -O  <key=value>            Overrides default parameter values.
  -P  <key=value>            Overrides default pre-clone assembler parameter values.
  -r, --report <path>        Report file (human readable version, see `-j / --json-report` for
                               machine readable report).
  -j, --json-report <path>   JSON formatted report file.
      --use-local-temp       Put temporary files in the same folder as the output files.
  -f, --force-overwrite      Force overwrite of output file(s).
      -nw, --no-warnings     Suppress all warning messages.
      --verbose              Verbose messages.
  -h, --help                 Show this help message and exit.
