@@ -47,7 +47,7 @@ For **pre-demultiplexed** data (prepared using external tools):
4747| -------------------- | ----------------------------------------------------------------------------------------------------------------- | ------------- |
4848| ` --demultiplexed ` | Whether input is multiplexed (` false ` , single FASTQ file) or pre-demultiplexed (` true ` , multiple FASTQ files) ^1^ | ` false ` |
4949| ` --lima_minscore ` | Barcode score for demultiplexing ^2^ | 93 |
50- | ` --lima_dualbarcode ` | Dual-barcoding scheme with identical barcodes at both ends ^3^ | ` true ` |
50+ | ` --lima_barcodetype ` | Barcoding scheme type ( ` single ` , ` dual ` , ` dual_symmetric ` , ` dual_asymmetric ` ) ^3^ | ` dual ` |
5151| ` --lima_W ` | Window size for barcode lookup | 70 |
5252| ` --lima_minlen ` | Minimum sequence length after clipping barcodes | 40 |
5353
@@ -69,9 +69,9 @@ For **pre-demultiplexed** data (prepared using external tools):
6969
7070^3^:
7171 Barcodes, which can also be referred to as adaptors, tags, indices, molecular identifiers (MIDs), come in various library designs.
72- At present, NextITS supports two barcoding schemes: dual-barcoding (which is the default ) and single-barcoding.
73- For the dual-barcoding scheme, the amplicon should have * the same barcode* on both ends.
74- An asymmetric design, where each side of the amplicon has a * different barcode pair* , is still in development .
72+ At present, NextITS supports 4 barcoding schemes: dual-barcoding (symmetric, assymetric, or mixture of combinatorial tags ) and single-barcoding.
73+ For the dual-barcoding scheme, the amplicon should have the barcode on both ends of the amplicon .
74+ An asymmetric design, where each side of the amplicon has a * different barcode pair* , is also supported .
7575 For a comprehensive understanding of barcode designs, please visit [ https://lima.how/barcode-design.html ] ( https://lima.how/barcode-design.html ) .
7676
7777
0 commit comments