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Update list of sequencers for poly-g trimming #508

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Merged
sfchen merged 3 commits into from
Jan 20, 2026
Merged

Update list of sequencers for poly-g trimming #508

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bb4ed45
Expand two-color SBS definitions
semenko Jul 14, 2023
00c3657
Merge branch 'OpenGene:master' into expand-polyg-trimming
semenko Jan 19, 2026
b3c14e0
Improve and expand sequencer list for poly-g trimming
semenko Jan 19, 2026
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21 changes: 17 additions & 4 deletions src/evaluator.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,10 +21,23 @@ 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")) {
delete r;
return true;
// Two-color system instrument prefixes
// See https://github.com/OpenGene/fastp/pull/508 for a detailed discussion
const vector<string> twoColorPrefixes = {
"@FS", // iSeq 100
"@MN", "@SH", // MiniSeq
"@NS", "@NB", // NextSeq 500/550
"@NDX", // NextSeq 550DX
"@VL", "@VH", // NextSeq 1000/2000
"@A", "@NA", // NovaSeq 6000
"@LH" // NovaSeq X
};

for (const string& prefix : twoColorPrefixes) {
if (starts_with(r->mName, prefix)) {
delete r;
return true;
}
}

delete r;
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