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upd params
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vmikk committed Nov 15, 2024
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Expand Up @@ -47,7 +47,7 @@ For **pre-demultiplexed** data (prepared using external tools):
| -------------------- | ----------------------------------------------------------------------------------------------------------------- | ------------- |
| `--demultiplexed` | Whether input is multiplexed (`false`, single FASTQ file) or pre-demultiplexed (`true`, multiple FASTQ files) ^1^ | `false` |
| `--lima_minscore` | Barcode score for demultiplexing ^2^ | 93 |
| `--lima_dualbarcode` | Dual-barcoding scheme with identical barcodes at both ends ^3^ | `true` |
| `--lima_barcodetype` | Barcoding scheme type (`single`, `dual`, `dual_symmetric`, `dual_asymmetric`) ^3^ | `dual` |
| `--lima_W` | Window size for barcode lookup | 70 |
| `--lima_minlen` | Minimum sequence length after clipping barcodes | 40 |

Expand All @@ -69,9 +69,9 @@ For **pre-demultiplexed** data (prepared using external tools):

^3^:
Barcodes, which can also be referred to as adaptors, tags, indices, molecular identifiers (MIDs), come in various library designs.
At present, NextITS supports two barcoding schemes: dual-barcoding (which is the default) and single-barcoding.
For the dual-barcoding scheme, the amplicon should have *the same barcode* on both ends.
An asymmetric design, where each side of the amplicon has a *different barcode pair*, is still in development.
At present, NextITS supports 4 barcoding schemes: dual-barcoding (symmetric, assymetric, or mixture of combinatorial tags) and single-barcoding.
For the dual-barcoding scheme, the amplicon should have the barcode on both ends of the amplicon.
An asymmetric design, where each side of the amplicon has a *different barcode pair*, is also supported.
For a comprehensive understanding of barcode designs, please visit [https://lima.how/barcode-design.html](https://lima.how/barcode-design.html).


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