| kit | No | a vendor kit id instead of a pasted list — the kit's own indexes are resolved and checked. Ignored when `pool` is given. Values: (No kit — paste a list instead), truseq-single-indexes (TruSeq Single Indexes — Illumina, 24 indexes), truseq-cd-indexes (TruSeq DNA and RNA CD Indexes — Illumina, 96 indexes), idt-truseq-ud-indexes (IDT for Illumina–TruSeq DNA and RNA UD Indexes — Illumina / IDT, 100 indexes), idt-illumina-ud-plate-a (IDT for Illumina UD Indexes, Plate A/Set 1 — Illumina / IDT, 96 indexes), idt-illumina-ud-plate-b (IDT for Illumina UD Indexes, Plate B/Set 2 — Illumina / IDT, 96 indexes), idt-illumina-ud-plate-c (IDT for Illumina UD Indexes, Plate C/Set 3 — Illumina / IDT, 98 indexes), idt-illumina-ud-plate-d (IDT for Illumina UD Indexes, Plate D/Set 4 — Illumina / IDT, 100 indexes). Only applies when pool is not given. | |
| pool | No | the pool as text — one row per sample: `name<TAB>i7[<TAB>i5]`, or bare index sequences one per line, with or without a header. Rows that cannot be read are REPORTED with their line number, never dropped. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| metric | No | error model the distance guarantee is measured under — a pool safe under substitutions may be unsafe under indels. Values: hamming (Hamming (substitutions)), seqlev (Sequence-Levenshtein (indels)), levenshtein (Levenshtein). | seqlev |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| i5_cycles | No | index-2 read length from the run recipe. 0 = use the indexes' own length. | |
| i7_cycles | No | index-1 read length from the RUN RECIPE, when it differs from the index length — a 10 nt index read at 8 cycles is an 8 nt index for every purpose here. 0 = use the indexes' own length. | |
| instrument | No | which instrument the run is on. It decides the chemistry the color balance is judged under AND the orientation index 2 is read in — a pool balanced on a NovaSeq 6000 is not balanced on a NovaSeq X. | NovaSeq X / X Plus |
| library_prep | No | which of Illumina's published hopping-rate classes applies. The check multiplies the published RANGE by what this pool can throw away, to report how much is unrecoverable — it never predicts a rate for your run. Values: patterned-examp (Patterned flow cell, ExAmp chemistry), truseq-pcr-free (TruSeq PCR-Free libraries). | patterned-examp |
| required_distance | No | the minimum distance the pool is SUPPOSED to guarantee, if it was designed to one — the check says whether it does. 0 = report the distance without judging it. Advanced. | |