Usage: mixcr [-h] [-v] [COMMAND]
  -h, --help      Show this help message and exit.
  -v, --version   Print version information and exit
Base commands:
  analyze            Run full MiXCR pipeline for specific input.
  align              Builds alignments with V,D,J and C genes for input sequencing reads.
  refineTagsAndSort  Applies error correction algorithm for tag sequences and sorts resulting file
                       by tags.
  assemblePartial    Assembles partially aligned reads into longer sequences.
  extend             Impute alignments or clones with germline sequences.
  assemble           Assemble clones.
  assembleContigs    Assemble full sequences.
  assembleCells      Group clones by cells. Required data with cell tags. All clones should be
                       fully covered by the same feature.
  findAlleles        Find allele variants in clnx.
  findShmTrees       Builds SHM trees.
  downsample         Downsample clonesets.
  qc                 Perform quality control checks on results.
Postanalysis commands:
  postanalysis  Run postanalysis routines. This command has subcommands, use -h to see more
Export commands:
  exportTables              CDR3 metrics, Diversity, V/J/VJ-Usage, CDR3/V-Spectratype, Overlap
  exportPreprocTables       Export preprocessing summary tables.
  exportPlots               Export postanalysis plots. This command has subcommands, use -h to see
                              more
  overlapScatterPlot        Plot overlap scatter-plot.
  exportAlignments          Export V/D/J/C alignments into tab delimited file.
  exportAlignmentsPretty    Export verbose information about alignments.
  exportClones              Export assembled clones into tab delimited file.
  exportCloneGroups         Export clone groups into tab delimited file. Data should be processed
                              by `assembleCells`
  exportClonesPretty        Export verbose information about clones.
  exportShmTreesWithNodes   Export SHMTree as a table with a row for every clone or reconstructed
                              node for each root (only one root if no single cell data)
  exportShmTrees            Export SHMTree as a table with a row for every SHM root in a table
                              (single row if no single cell data)
  exportShmSingleCellTrees  Export SHM trees with one row per node. Tree may contain several roots,
                              that will be exported in separate columns. Initial data for building
                              tree should contain cell data.
  exportShmTreesNewick      Export SHMTree as newick
  exportReports             Export MiXCR reports.
  exportReportsTable        Export reports from files in tabular format.
  exportQc                  Export QC plots. This command has subcommands, use -h to see more
  exportClonesOverlap       Build cloneset overlap and export into tab delimited file.
  exportAirr                Exports a clns, clna or vdjca file to Airr formatted tsv file.
Util commands:
  exportReadsForClones       Export reads for particular clones from "clones & alignments" (*.clna)
                               file.
  exportAlignmentsForClones  Export alignments for particular clones from "clones & alignments" (*.
                               clna) file.
  exportReads                Export original reads from vdjca file.
  mergeAlignments            Merge several *.vdjca files with alignments into a single alignments
                               file.
  filterAlignments           Filter alignments.
  sortAlignments             Sort alignments in vdjca file by read id.
  sortClones                 Sort clones by sequence. Clones in the output file will be sorted by
                               clonal sequence, which allows to build overlaps between clonesets.
  alignmentsDiff             Calculates the difference between two .vdjca files.
  clonesDiff                 Calculates the difference between two .clns files.
  versionInfo                Output information about MiXCR version which generated the file.
  slice                      Slice vdjca|clns|clna|shmt file.
  exportPreset               Export a preset file given the preset name or source file and a set of
                               mix-ins
  buildLibrary               Build custom reference library
  mergeLibrary               Merge multiple reference libraries in one file
  debugLibrary               Debug reference library file
  listPresets                Show all available presets
