diff --git a/docs/parameters.md b/docs/parameters.md index a134487..6f6e4cc 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -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 | @@ -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).