Usage: mixcr align --preset <preset> [--strict-sample-sheet-matching] [--trimming-quality-threshold
                   <n>] [--trimming-window-size <n>] [--write-all] [--tag-pattern-file <path>]
                   [--tag-parse-unstranded] [--tag-max-budget <n>] [--read-id-as-cell-tag]
                   [--read-buffer <n>] [--high-compression] [--reference-for-cram genome.fasta[.
                   gz]] [--not-aligned-I1 <path.fastq[.gz]>] [--not-aligned-I2 <path.fastq[.gz]>]
                   [--not-aligned-R1 <path.fastq[.gz]>] [--not-aligned-R2 <path.fastq[.gz]>]
                   [--not-parsed-I1 <path.fastq[.gz]>] [--not-parsed-I2 <path.fastq[.gz]>]
                   [--not-parsed-R1 <path.fastq[.gz]>] [--not-parsed-R2 <path.fastq[.gz]>]
                   [--species <species>] [--library <library>] [--split-by-sample]
                   [--dont-split-by-sample] [--sample-sheet sample_sheet.tsv]
                   [--sample-sheet-strict sample_sheet.tsv] [--dna] [--rna]
                   [--floating-left-alignment-boundary [<anchor_point>]]
                   [--rigid-left-alignment-boundary [<anchor_point>]]
                   [--floating-right-alignment-boundary (<gene_type>|<anchor_point>)]
                   [--rigid-right-alignment-boundary [(<gene_type>|<anchor_point>)]] [--tag-pattern
                   <pattern>] [--keep-non-CDR3-alignments] [--drop-non-CDR3-alignments]
                   [--limit-input <n>] [--set-whitelist <key=value>] [--reset-whitelist <tag_name>]
                   [--dont-correct-tag-with-name <tag_name>] [--dont-correct-tag-type
                   (Molecule|Cell|Sample)] [--assemble-clonotypes-by <gene_features>]
                   [--split-clones-by <gene_type>]... [--dont-split-clones-by <gene_type>]...
                   [--assemble-contigs-by <gene_features>] [--assemble-longest-contigs]
                   [--impute-germline-on-export] [--dont-impute-germline-on-export]
                   [--prepend-export-clones-field <field> [<param>...]]...
                   [--append-export-clones-field <field> [<param>...]]...
                   [--prepend-export-clone-groups-field <field> [<param>...]]...
                   [--append-export-clone-groups-field <field> [<param>...]]...
                   [--prepend-export-alignments-field <field> [<param>...]]...
                   [--append-export-alignments-field <field> [<param>...]]...
                   [--add-export-clone-table-splitting <(geneLabel|tag):key>]
                   [--reset-export-clone-table-splitting] [--add-export-clone-grouping <
                   (geneLabel|tag):key>] [--reset-export-clone-grouping] [--filter-out-group-types
                   (found|undefined|contamination)]... [--reset-group-types-filter]
                   [--export-productive-clones-only] [--export-clone-groups-for-cell-type
                   <cell_type>]... [--export-clone-groups-for-all-cell-types]
                   [--show-secondary-chain-on-export-cell-groups]
                   [--dont-show-secondary-chain-on-export-cell-groups]
                   [--export-clone-groups-sort-chains-by (Read|Molecule|Auto)] [-O <key=value>]...
                   [--report <path>] [--json-report <path>] [--use-local-temp] [--threads <n>]
                   [--force-overwrite] [--no-warnings] [--verbose] [--help] [-M <key=value>]...
                   [--remove-qc-check <type> [--remove-qc-check <type>]...]... ([file_I1.fastq[.gz]
                   [file_I2.fastq[.gz]]] file_R1.fastq[.gz] [file_R2.fastq[.gz]]|file.(fasta[.gz]
                   |bam|sam|cram)) alignments.vdjca
Builds alignments with V,D,J and C genes for input sequencing reads.
      ([file_I1.fastq[.gz] [file_I2.fastq[.gz]]] file_R1.fastq[.gz] [file_R2.fastq[.gz]]|file.(fasta
        [.gz]|bam|sam|cram))
                             Two fastq files for paired reads or one file for single read data.
                             Use {{n}} if you want to concatenate files from multiple lanes, like:
                             my_file_L{{n}}_R1.fastq.gz my_file_L{{n}}_R2.fastq.gz
      alignments.vdjca       Path where to write output alignments
  -p, --preset <preset>      Analysis preset. Sets key parameters of this and all downstream
                               analysis steps. It is critical to carefully select the most
                               appropriate preset for the data you analyse.
      --strict-sample-sheet-matching
                             Perform strict matching against input sample sheet (one substitution
                               will be allowed by default).
                             This option only valid if input file is *.tsv sample sheet.
      --trimming-quality-threshold <n>
                             Read pre-processing: trimming quality threshold. Zero value can be
                               used to skip trimming.
                               Default value determined by the preset.
      --trimming-window-size <n>
                             Read pre-processing: trimming window size.
                               Default value determined by the preset.
      --write-all            Write alignment results for all input reads (even if alignment failed).
                               Default value determined by the preset.
      --tag-pattern-file <path>
                             Read tag pattern from a file.
                               Default value determined by the preset.
      --tag-parse-unstranded If paired-end input is used, determines whether to try all
                               combinations of mate-pairs or only match reads to the corresponding
                               pattern sections (i.e. first file to first section etc).
                               Default value determined by the preset.
      --tag-max-budget <n>   Maximal bit budget controlling mismatches (substitutions) in tag
                               pattern. Higher values allows more substitutions in small letters.
                               Default value determined by the preset.
      --read-id-as-cell-tag  Marks reads, coming from different files, but having the same
                               positions in those files, as reads coming from the same cells. Main
                               use-case is protocols with overlapped alpha-beta, gamma-delta or
                               heavy-light cDNA molecules, where each side was sequenced by
                               separate mate pairs in a paired-end sequencer. Use special expansion
                               group CELLSPLIT instead of R index (i.e. "my_file_R{{CELLSPLIT:n}}.
                               fastq.gz").
                               Default value determined by the preset.
      --read-buffer <n>      Size of buffer for FASTQ readers in bytes. Default: 4Mb
      --high-compression     Use higher compression for output file, 10~25% slower, minus 30~50% of
                               file size.
      --reference-for-cram genome.fasta[.gz]
                             Reference to the genome that was used for build a cram file
      --not-aligned-I1 <path.fastq[.gz]>
                             Pipe not aligned I1 reads into separate file.
      --not-aligned-I2 <path.fastq[.gz]>
                             Pipe not aligned I2 reads into separate file.
      --not-aligned-R1 <path.fastq[.gz]>
                             Pipe not aligned R1 reads into separate file.
      --not-aligned-R2 <path.fastq[.gz]>
                             Pipe not aligned R2 reads into separate file.
      --not-parsed-I1 <path.fastq[.gz]>
                             Pipe not parsed I1 reads into separate file.
      --not-parsed-I2 <path.fastq[.gz]>
                             Pipe not parsed I2 reads into separate file.
      --not-parsed-R1 <path.fastq[.gz]>
                             Pipe not parsed R1 reads into separate file.
      --not-parsed-R2 <path.fastq[.gz]>
                             Pipe not parsed R2 reads into separate file.
  -s, --species <species>    Species (organism). Possible values: `hsa` (or HomoSapiens), `mmu` (or
                               MusMusculus), `rat`, `spalax`, `alpaca`, `lamaGlama`, `mulatta`
                               (_Macaca Mulatta_), `fascicularis` (_Macaca Fascicularis_) or any
                               species from IMGT ® library.
  -b, --library <library>    V/D/J/C gene library. By default, the `default` MiXCR reference
                               library is used. One can also use external libraries
      --split-by-sample      Split output alignments files by sample.
      --dont-split-by-sample Don't split output alignments files by sample.
      --sample-sheet sample_sheet.tsv
                             Loads sample table from a tab separated file (one substitution will be
                               allowed during matching)
      --sample-sheet-strict sample_sheet.tsv
                             Loads sample table from a tab separated file (strict matching will be
                               used).
      --dna                  For DNA starting material. Setups V gene feature to align to
                               `VGeneWithP` (full intron) and also instructs MiXCR to skip C gene
                               alignment since it is too far from CDR3 in DNA data.
      --rna                  For RNA starting material; setups `VTranscriptWithP` (full exon) gene
                               feature to align for V gene and `CExon1` for C gene.
      --floating-left-alignment-boundary [<anchor_point>]
                             Configures aligners to use semi-local alignment at reads 5'-end.
                               Typically used with V gene single primer / multiplex protocols, or
                               if there are non-trimmed adapter sequences at 5'-end. Optional
                               <anchor_point> may be specified to instruct MiXCR where the primer
                               is located and strip V feature to align accordingly, resulting in a
                               more precise alignments.
      --rigid-left-alignment-boundary [<anchor_point>]
                             Configures aligners to use global alignment at reads 5'-end. Typically
                               used for 5'RACE with template switch oligo or a like protocols.
                               Optional <anchor_point> may be specified to instruct MiXCR how to
                               strip V feature to align.
      --floating-right-alignment-boundary (<gene_type>|<anchor_point>)
                             Configures aligners to use semi-local alignment at reads 3'-end.
                               Typically used with J or C gene single primer / multiplex protocols,
                               or if there are non-trimmed adapter sequences at 3'-end. Requires
                               either gene type (`J` for J primers / `C` for C primers) or
                               <anchor_point> to be specified. In latter case MiXCR will
                               additionally strip feature to align accordingly.
      --rigid-right-alignment-boundary [(<gene_type>|<anchor_point>)]
                             Configures aligners to use global alignment at reads 3'-end. Typically
                               used for J-C intron single primer / multiplex protocols. Optional
                               <gene_type> (`J` for J primers / `C` for C primers) or
                               <anchor_point> may be specified to instruct MiXCR where how to strip
                               J or C feature to align.
      --tag-pattern <pattern>
                             Specify tag pattern for barcoded data.
      --keep-non-CDR3-alignments
                             Preserve alignments that do not cover CDR3 region or cover it only
                               partially in the .vdjca file.
      --drop-non-CDR3-alignments
                             Drop all alignments that do not cover CDR3 region or cover it only
                               partially.
      --limit-input <n>      Maximal number of reads to process on `align`
      --remove-qc-check <type>
                             Remove qc check with given type. Use `exportPreset` command to see
                               what `qc.checks` are included in the preset.
  -O  <key=value>            Overrides aligner parameters from the selected preset
  -M  <key=value>            Overrides arbitrary preset parameter
  -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.
  -t, --threads <n>          Processing threads
  -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.
Params for refineTagsAndSort command:
      --set-whitelist <key=value>
                             Sets the whitelist for a specific tag to guide the tag refinement
                               procedure.
                             Usage: --set-whitelist CELL=preset:737K-august-2016 or --set-whitelist
                               UMI=file:my_umi_whitelist.txt .
      --reset-whitelist <tag_name>
                             Resets the whitelist for a specific tag so that unguided refinement
                               procedure will be applied for it
      --dont-correct-tag-with-name <tag_name>
                             Don't correct alignments for tag
      --dont-correct-tag-type (Molecule|Cell|Sample)
                             Don't correct alignments for tag type
Params for assemble command:
      --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.
Params for assembleContigs command:
      --assemble-contigs-by <gene_features>
                             Selects the region of interest for the action. Clones will be
                               separated if inconsistent nucleotides will be detected in the
                               region, assembling procedure will be limited to the region, and only
                               clonotypes that fully cover the region will be outputted, others
                               will be filtered out.
      --assemble-longest-contigs
                             Contigs with maximum possible length will be assembled.
Params for export commands:
      --impute-germline-on-export
                             Export nucleotide sequences using letters from germline (marked
                               lowercase) for uncovered regions
      --dont-impute-germline-on-export
                             Export nucleotide sequences only from covered region
      --prepend-export-clones-field <field> [<param>...]
                             Add clones export column before other columns. First param is field
                               name as it is in `exportClones` command, left params are params of
                               the field
      --append-export-clones-field <field> [<param>...]
                             Add clones export column after other columns. First param is field
                               name as it is in `exportClones` command, left params are params of
                               the field
      --prepend-export-clone-groups-field <field> [<param>...]
                             Add clone groups export column before other columns. First param is
                               field name as it is in `exportCloneGroups` command, left params are
                               params of the field
      --append-export-clone-groups-field <field> [<param>...]
                             Add clone groups export column after other columns. First param is
                               field name as it is in `exportCloneGroups` command, left params are
                               params of the field
      --prepend-export-alignments-field <field> [<param>...]
                             Add clones export column before other columns. First param is field
                               name as it is in `exportAlignments` command, left params are params
                               of the field
      --append-export-alignments-field <field> [<param>...]
                             Add clones export column after other columns. First param is field
                               name as it is in `exportAlignments` command, left params are params
                               of the field
      --add-export-clone-table-splitting <(geneLabel|tag):key>
                             Add key to split output files with clone tables.
      --reset-export-clone-table-splitting
                             Reset all file splitting for output clone and/or clone group tables.
      --add-export-clone-grouping <(geneLabel|tag):key>
                             Add key to group clones in the output clone tables.
      --reset-export-clone-grouping
                             Reset all clone grouping in the output clone tables.
      --filter-out-group-types (found|undefined|contamination)
                             Filter out clones from groups of particular type.
                             `found` - groups that were found on `assembleCells`.
                             `undefined` - there were not enough info on `assembleCells` to form a
                               group.
                             `contamination` - clones that were marked as contamination on
                               `assembleCells`.
      --reset-group-types-filter
                             Reset filter of clones by group type.
      --export-productive-clones-only
                             Export only productive clonotypes.
      --export-clone-groups-for-cell-type <cell_type>
                             Export clone groups for given cell type.
                             If selected only one cell type, export will be written in one file
                               without prefixes. If several, there will be a file for each type.
                             All cell groups that don't much specified groups will be filtered out.
                             Possible values: IGH-IGK, IGH-IGL, TRB-TRA, TRD-TRG.
      --export-clone-groups-for-all-cell-types
                             Export clone groups for all cell types.
      --show-secondary-chain-on-export-cell-groups
                             Show columns for secondary chains in export for cell groups.
      --dont-show-secondary-chain-on-export-cell-groups
                             Don't show columns for secondary chains in export for cell groups.
      --export-clone-groups-sort-chains-by (Read|Molecule|Auto)
                             How to sort clones for determination of the primary and the secondary
                               chains.
                             Read - by reads count, Molecule - by count of UMI tags, Auto - by UMI
                               if it's available, by Read otherwise
