Adapter Schemes

CutSeq supports a variety of built-in adapter schemes for common NGS library types. You can list all available schemes in your terminal with:

cutseq --list-adapters

Use the adapter name with -A/--adapter-name, or specify a custom scheme string with -a/--adapter-scheme.

Example: Built-in Schemes

  • SMALLRNA: Small RNA libraries, double ligation, forward orientation
  • INLINE: Custom barcoded libraries, dual UMI, inline barcode
  • TAKARAV3: SMARTer Stranded Total RNA-Seq Kit v3
  • STRANDED: Stranded RNA libraries

See below for a comprehensive guide to each supported adapter pattern, including copyable scheme blocks and usage notes.

SMALLRNA (Small RNA Libraries)

AGTTCTACAGTCCGACGATC
>
AGATCGGAAGAGCACACGTC
  • Used for small RNA sequencing
  • Double ligation method
  • Forward orientation
  • Optional 2nt trimming on both ends for quality

SMRNA (Small RNA, Legacy version)

AGTTCTACAGTCCGACGATC
>
TGGAATTCTCGGGTGCCAAG
  • Legacy version for small RNA sequencing
  • Refer to library preparation protocol for details.

INLINE (Custom Barcoded Libraries)

AGTTCTACAGTCCGACGATCNNNNN
>
NNNNNATCACGAGATCGGAAGAGCACACGTC
  • Used for libraries with inline barcodes
  • Dual UMI design (5nt each)
  • Forward orientation
  • Contains fixed inline barcode (ATCACG)

TAKARAV2 (Takara V2)

ACACGACGCTCTTCCGATCTXXX
<
XXXAGATCGGAAGAGCACACGTC
  • Contains masked regions (XXX)
  • Refer to Takara V2 library preparation protocol for details.

STRANDED (Stranded RNA)

ACACGACGCTCTTCCGATCTX
<
XXXAGATCGGAAGAGCACACGTC
  • Contains masked regions (X, XXX)
  • Refer to stranded RNA library preparation protocol for details.

UNSTRANDED (Unstranded RNA/DNA)

ACACGACGCTCTTCCGATCTXX
-
XXAGATCGGAAGAGCACACGTC
  • Contains masked regions (XX)
  • Refer to library preparation protocol for details.

TAKARAV3 (Takara V3)

ACACGACGCTCTTCCGATCTXXX
<
XXXXXXNNNNNNNNAGATCGGAAGAGCACACGTC
  • Contains masked regions (XXX, XXXXXX)
  • Contains UMI sequences (NNNNNNNN)
  • Refer to Takara V3 library preparation protocol for details.

ECLIP6 (eCLIP (6nt UMI))

ACACGACGCTCTTCCGATCTXX
<
XNNNNNNAGATCGGAAGAGCACACGTC
  • Contains masked regions (XX, X)
  • Contains UMI sequences (NNNNNN)
  • Used for eCLIP experiments with a 6-nucleotide UMI.

ECLIP10 (eCLIP (10nt UMI))

ACACGACGCTCTTCCGATCTXX
<
XNNNNNNNNNNAGATCGGAAGAGCACACGTC
  • Contains masked regions (XX, X)
  • Contains UMI sequences (NNNNNNNNNN)
  • Used for eCLIP experiments with a 10-nucleotide UMI.

SACSEQ (SAC-Seq)

ACACGACGCTCTTCCGATCT
<
XXXXNNNNNNAGATCGGAAGAGCACACGTC
  • Contains masked regions (XXXX)
  • Contains UMI sequences (NNNNNN)
  • Used for SAC-Seq (Single-cell RNA-Seq) or similar protocols.

SACSEQV3 (SAC-Seq V3)

ACACGACGCTCTTCCGATCTNNNNNNNNX
>
XXNNNNNNNNAGATCGGAAGAGCACACGTC
  • Contains masked regions (X, XX)
  • Contains dual UMI sequences (NNNNNNNN on both sides)
  • Refer to SAC-Seq V3 library preparation protocol for details.

XGENRNA (xGen RNA)

ACACGACGCTCTTCCGATCTXXXXXX
<
XXXXXXXXXXXXXXXAGATCGGAAGAGCACACGTC
  • Contains extensive masked regions (XXXXXX, XXXXXXXXXXXXXXX)
  • Refer to xGen™ RNA Library Preparation Kit protocol for details.

ILLUMINARNA (Illumina Stranded RNA (Nextera-based))

AGATGTGTATAAGAGACAG
<
CTGTCTCTTATACACATCT
  • Uses Nextera-style adapter sequences.

DSLIGATION (dsDNA Ligation)

ACACGACGCTCTTCCGATCT
>
AGATCGGAAGAGCACACGTC
  • Basic dsDNA ligation with A-tailing
  • No UMIs or special trimming needed

XGENMETHY (xGen Methyl-Seq)

ACACGACGCTCTTCCGATCTXX
>
XXXXXXXXXXAGATCGGAAGAGCACACGTC
  • Contains masked regions (XX, XXXXXXXXXX)
  • Designed for xGen Methyl-Seq library kits.

XGENSNMC (xGen snmC-Seq)

ACACGACGCTCTTCCGATCTXXXXXX
>
XXXXXXXXXXXXXXXAGATCGGAAGAGCACACGTC
  • Contains extensive masked regions (XXXXXX, XXXXXXXXXXXXXXX)
  • Designed for xGen single-nucleus methylC-Seq (snmC-Seq) library kits.

PBAT (PBAT (Post-Bisulfite Adapter Tagging))

ACACGACGCTCTTCCGATCTXXXXXX
<
XXXXXXAGATCGGAAGAGCACACGTC
  • Contains masked regions (XXXXXX on both sides)
  • Used for PBAT-style bisulfite sequencing libraries.

NEXTERA (Nextera (General))

AGATGTGTATAAGAGACAG
>
CTGTCTCTTATACACATCT
  • Standard Nextera transposase-based library preparation.
  • No UMIs by default in this basic scheme.
  • Usually used for ATAC-seq libraries.

Copyright © 2021-2024, Chang Ye