From bb4ed4551b46c45697bbc557c8fbd2165ee6ffbb Mon Sep 17 00:00:00 2001 From: Nick Semenkovich Date: Fri, 14 Jul 2023 06:13:12 -0500 Subject: [PATCH] Expand two-color SBS definitions Expanded parsing of Illumina 2-color SBS definitions for poly-g trimming. These values are via: https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000003880 This expands the previous 2-color list by adding: Novaseq 1000/2000 (@VL @VH) Novaseq X Plus (@LH) This changes the Novaseq 6000 header from (@A0 to @A) per Illumina's doc. (I do not see @NDX documented by illumina, but this might be their NextSeq 550Dx FDA-regulated sequencer.) --- src/evaluator.cpp | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/src/evaluator.cpp b/src/evaluator.cpp index 48bca94f..ea1620b5 100644 --- a/src/evaluator.cpp +++ b/src/evaluator.cpp @@ -21,8 +21,13 @@ bool Evaluator::isTwoColorSystem() { if(!r) return false; - // NEXTSEQ500, NEXTSEQ 550/550DX, NOVASEQ - if(starts_with(r->mName, "@NS") || starts_with(r->mName, "@NB") || starts_with(r->mName, "@NDX") || starts_with(r->mName, "@A0")) { + // Via https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000003880 + // NEXTSEQ 500/550: @NS @NB + // ? NEXTSEQ 550DX: @NDX + // NEXTSEQ 1000/2000: @VL @VH + // NOVASEQ 6000: @A + // NOVASEQ X PLUS: @LH + if(starts_with(r->mName, "@NS") || starts_with(r->mName, "@NB") || starts_with(r->mName, "@NDX") || starts_with(r->mName, "@VL") || starts_with(r->mName, "@VH") || starts_with(r->mName, "@A") || starts_with(r->mName, "@LH")) { delete r; return true; }