Glossary ======== Terms used throughout these pages, in the sense arda uses them. .. glossary:: :sorted: AIRR Rearrangement The `AIRR Community `_ standard schema for one annotated receptor sequence: gene calls, region coordinates, the junction and its translation, with defined column names and value formats. Every per-sequence TSV arda writes is a valid AIRR Rearrangement file. See :doc:`outputs`. allele The most specific level of IMGT gene nomenclature, written with a ``*`` suffix: ``TRBV19*01``. Separating a gene's alleles usually needs substantially more read coverage than naming the gene — see :doc:`genotype`. amplicon A targeted library in which nearly every read is receptor-derived and reads span V into J, produced by multiplex V primers or 5'RACE. Sometimes called RepSeq. Handled by :ref:`arda amplicon `. anchor The conserved residue that bounds the junction: Cys104 on the V side, Phe or Trp 118 on the J side, in IMGT numbering. arda stores the anchor position and templated residues per allele in ``cdr3_anchors.tsv`` and refuses to emit a junction whose V anchor the read never reached. bulk RNA-seq A whole-transcriptome library in which 0.02–3 % of reads are receptor-derived and a read lands anywhere in a transcript rather than spanning V into J. Handled by :ref:`arda rnaseq `. CDR3 Complementarity-determining region 3, in the IMGT definition: the junction **excluding** both conserved anchors. See :term:`junction` — the two differ by two residues and conflating them corrupts every downstream coordinate. chimera A clonotype whose V and J calls come from loci that cannot rearrange together. arda counts them in :doc:`qc` and flags them; it never removes them. clonotype A group of reads collapsed onto one rearrangement. The grouping key is set by ``--clonotype-key``: ``full`` (locus, V, J, junction) by default, or ``junction`` alone. One row of ``.clones.tsv``. consensus_count AIRR column: the number of distinct fragments supporting a clonotype. Use it when you need molecules. Compare :term:`duplicate_count`. duplicate_count AIRR column: the number of reads encompassing the junction of a clonotype. arda's expression estimate. Use it when you need abundance. Invariant across every ``--ec-mode`` — error correction moves reads onto a parent, it never discards them. ec-mode The denoising preset given to ``arda correct`` (``--ec-mode``). Chosen from what the answer will be used for, not from the library type. See :doc:`error_correction`. fast_fraction Reported in ``.arda.json``: the fraction of reads that hit **both** a V and a J segment in the two-pass search. It predicts whether the amplicon speed configuration will pay, better than the library's name does. Roughly .85 on a primer-anchored TCR amplicon, .50 on IGH RepSeq, .05 on bulk. IMGT The `international ImMunoGeneTics information system `_: the source of arda's germline sequences and of the region and numbering conventions it follows. junction The nucleotide (or amino acid) stretch from Cys104 through Phe/Trp118 **inclusive of both anchors**. This is what AIRR calls ``junction`` and what MiXCR labels ``CDR3``. It is two residues longer than IMGT :term:`CDR3`, which arda writes separately as ``cdr3``. J+C scaffold A reference entry consisting of a J germline with the CH1 constant exon spliced onto it, and no V. It gives reads that span the J→C splice — which end in the constant region and have no V to anchor on — somewhere to map, and is what lets arda report a ``c_call`` for them. 345 of them ship for human. locus The receptor chain a sequence belongs to: ``TRA``, ``TRB``, ``TRG``, ``TRD``, ``IGH``, ``IGK``, ``IGL``. arda searches all of them at once and reports the one that won. mode One of ``arda rnaseq``, ``arda amplicon``, ``arda cells``. The mode name carries the speed configuration for its library type, because the configurations do not compose. See :doc:`usage`. read group One ``(R1, R2)`` FASTQ pair belonging to a sample. A sample delivered as several Illumina lanes is one repertoire made of several read groups; arda maps each and concatenates before clonotype calling. See :doc:`samples`. regime The library class a speed configuration is tuned for — bulk or amplicon. Named once in ``arda.cluster.regime_flags`` so the CLI, SLURM, Nextflow and Snakemake cannot disagree. scaffold A reference entry made of one V allele and one J allele joined in frame, with a short frame-neutral N spacer where D would sit, carrying IgBLAST-derived FR1–FR4 / CDR1–CDR3 coordinates. Queries are mapped to scaffolds and the markup is projected back onto them. 15,069 V·J scaffolds ship for human. segment A single germline allele (V, J or C) in the collapsed 924-target reference that the two-pass search screens against, as opposed to a full V·J :term:`scaffold`. SHM Somatic hypermutation: the AID-driven mutation of rearranged IG loci in germinal centres. arda reports it as ``v_identity``, ``v_mutations`` and ``j_mutations``, scoped outside the junction by default. See :doc:`shm`. stage One of the three steps a mode runs: ``map`` (Stage 1, per read), ``correct`` (Stage 2, global), ``assemble`` (Stage 3, global). Each is also a standalone command, which is what makes sharding possible. tie list A comma-joined set of gene or allele names that the alignment cannot separate, written into a single ``v_call`` / ``j_call`` / ``d_call`` field. Standard AIRR practice; scoring a tie list as a miss is a scoring artifact rather than a calling error. UMI Unique molecular identifier: a random barcode attached to a cDNA molecule before amplification, used to collapse PCR duplicates into one consensus. arda does not collapse UMIs; ``arda cells`` consumes the consensus an upstream tool produced.