Commit da25d7dc authored by Mathieu Giraud's avatar Mathieu Giraud

doc/vidjil-algo.md: details, typos

parent 04507580
Pipeline #45019 failed with stages
in 26 minutes and 52 seconds
......@@ -645,15 +645,15 @@ See also [What is a clone ?](vidjil-format/#what-is-a-clone).
| ----- | ---- | ------------------------------------------------------- |
| locus | string | Gene locus (chain type). For example, `IGH`, `IGK`, `IGL`, `TRA`, `TRB`, `TRD`, or `TRG`.<br />*Vidjil-algo outputs all these loci. Moreover, the incomplete recombinations analyzed by vidjil-algo are reported as `IGH+`, `IGK+`, `TRA+D`, `TRB+`, `TRD+`, and `xxx` for unexpected recombinations. See [locus](locus).*
| consensus_count | number | Number of reads contributing to the (UMI) consensus for this sequence. For example, the sum of the number of reads for all UMIs that contribute to the query sequence. <br />*Number of reads gathered in the clone.*
| consensus_ratio (+) | number | *Ratio of the number of reads gathered in the clone against the total number of reads analyzed with recombinations.*
| sequence_id | string | Unique query sequence identifier within the file. Most often this will be the input sequence header or a substring thereof, but may also be a custom identifier defined by the tool in cases where query sequences have been combined in some fashion prior to alignment. <br />*This identifier is the (50 bp by default) window extacted around the junction.* |
| clone_id | string | Clonal cluster assignment for the query sequence. <br />*This identifier is again the (50 bp by default) window extacted around the junction.*
| warnings (+) | string | *Warnings associated to this clone. See <https://gitlab.vidjil.org/blob/dev/doc/warnings.md>.*
| sequence | string | The query nucleotide sequence. Usually, this is the unmodified input sequence, which may be reverse complemented if necessary. In some cases, this field may contain consensus sequences or other types of collapsed input sequences if these steps are performed prior to alignment. <br />*This contains the consensus/representative sequence of each clone.*
| rev_comp | boolean | True if the alignment is on the opposite strand (reverse complemented) with respect to the query sequence. If True then all output data, such as alignment coordinates and sequences, are based on the reverse complement of 'sequence'. <br />*Set to null, as vidjil-algo gather reads from both strands in clones* |
| v_call, d_call, j_call | string | V/D/J gene with allele. For example, IGHV4-59\*01. <br /> *In the case of uncomplete/unexpected recombinations (locus with a `+`), we still use* `v/d/j_call`. |
junction | string | Junction region nucleotide sequence, where the junction is defined as the CDR3 plus the two flanking conserved codons. <br />*null*
| junction_aa | string | Junction region amino acid sequence. <br />*null*
| junction | string | Junction region nucleotide sequence, where the junction is defined as the CDR3 plus the two flanking conserved codons. <br />*null*
| junction_aa | string | Junction region amino acid sequence. <br />*implemented*
| cdr3_aa | string | Amino acid translation of the cdr3 field. <br />*implemented*
| productive | boolean | True if the V(D)J sequence is predicted to be productive. <br /> *true, false, or null when no CDR3 has been detected* |
| sequence_alignment | string | Aligned portion of query sequence, including any indel corrections or numbering spacers, such as IMGT-gaps. Typically, this will include only the V(D)J region, but that is not a requirement. <br /> *null* |
| germline_alignment | string | Assembled, aligned, fully length inferred germline sequence spanning the same region as the sequence_alignment field (typically the V(D)J region) and including the same set of corrections and spacers (if any). <br />*null*
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