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Warn if adapters cannot be indexed #823

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marcelm opened this issue Dec 5, 2024 · 0 comments
Open

Warn if adapters cannot be indexed #823

marcelm opened this issue Dec 5, 2024 · 0 comments

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@marcelm
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marcelm commented Dec 5, 2024

When providing lots of 5' anchored adapters with -e 2, an index can be generated and finding the adapters (barcodes) is fast. When then the maximum allowed number of errors is increased (say with -e 3), no index is generated (because an index is only generated up to two allowed errors), which has two consequences:

  • Matching becomes slow
  • Possibly ambiguous adapter/barcode assignments are no longer detected

We cannot always warn when no index can be created, but maybe when there are at least a certain number of anchored sequences and only the error rate is too high.

CC @simonelsasser
CC @cnluzon

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