📚 Adapter Schemes
CutSeq supports various built-in adapter schemes for different NGS library preparation methods. Each scheme follows a general pattern:
Components
- p5: 5’ Illumina sequencing adapter (shown in light green)
- p7: 3’ Illumina sequencing adapter (shown in pale green)
- inline5: Fixed DNA barcode sequences in brackets () (shown in light cyan)
- inline3: Fixed DNA barcode sequences in brackets () (shown in light sky blue)
- umi5: 5’ Random UMI sequences marked as N (shown in dodger blue)
- umi3: 3’ Random UMI sequences marked as N (shown in steel blue)
- mask5: Sequences to be masked marked as X (shown in gainsboro)
- mask3: Sequences to be masked marked as X (shown in light gray)
- strand: Direction indicator (shown with >, <, or -)
Built-in Schemes
DSLIGATION (dsDNA Ligation)
AGTTCTACAGTCCGACGATC
>
AGATCGGAAGAGCACACGTC - Basic dsDNA ligation with A-tailing
- Forward orientation
- No UMIs or special trimming needed
SMALLRNA (Small RNA Libraries)
AGTTCTACAGTCCGACGATC
>
AGATCGGAAGAGCACACGTC - Used for small RNA sequencing
- Double ligation method
- Forward orientation
- Optional 2nt trimming on both ends for quality
INLINE (Custom Barcoded Libraries)
AGTTCTACAGTCCGACGATC NNNNN
>
NNNNN (ATCACG) AGATCGGAAGAGCACACGTC - Used for libraries with inline barcodes
- Dual UMI design (5nt each)
- Forward orientation
- Contains fixed barcode sequence
TAKARAV2 (SMARTer® Stranded Protocol V2)
ACACGACGCTCTTCCGATCT XXXXXX
<
XXXXXX AGATCGGAAGAGCACACGTC - Handles polyC/G artifacts from random RT priming
- Extended masking for adaptase tail (up to 15bp)
- Reverse orientation
- Uses random polyC tail as pseudo-UMI
PBAT (Post-Bisulfite Adapter Tagging)
ACACGACGCTCTTCCGATCT XXXXXX
<
XXXXXX AGATCGGAAGAGCACACGTC - Used for post-bisulfite DNA sequencing
- Random primer-based adapter addition
- Reverse orientation
- Symmetric masking for random tails
NEXTERA (ATAC-seq)
AGATGTGTATAAGAGACAG
>
CTGTCTCTTATACACATCT - Used for ATAC-seq libraries
- Simple design without UMIs or barcodes
- Forward orientation
- Standard Nextera adapters
ILLUMINARNA (Illumina Stranded RNA-Seq)
AGATGTGTATAAGAGACAG
<
CTGTCTCTTATACACATCT - Standard Illumina stranded RNA-seq protocol
- Reverse orientation
- Simple design without UMIs or masking
- Direct adapter ligation method