Issues

• Absolute number of errors (-e N) is one too small for some adapter lengths (e.g. -e 1 allows 0 errors for a 49 nt adapter)

  marcelm/cutadapt#892 · Filter by author cindykrafft opened on Sep 3, 2026

• documentation for using info-file with linked adapters

  marcelm/cutadapt#890 · Filter by author chucknordy opened on Aug 15, 2026

• Error when combining multiple 5' adapter search with -g file: and ;rightmost

  marcelm/cutadapt#889 · Filter by author clmattson opened on Jul 31, 2026

• Question: Combinatorial multiplexing on single reads

  marcelm/cutadapt#887 · Filter by author Auerilas opened on Jun 30, 2026
  1

• Questions about parameters -a and -O

  marcelm/cutadapt#884 · Filter by author duzc-Repos opened on May 9, 2026

• Some polyGs at the end of the sequences are not removed

  marcelm/cutadapt#883 · Filter by author saharbagheri opened on May 6, 2026

• Feature request: empirical sequencing-error-rate estimation

  marcelm/cutadapt#881 · Filter by author jdidion opened on May 4, 2026

• Adapter trimming and demultiplexing

  marcelm/cutadapt#880 · Filter by author owen-hughes42 opened on Apr 30, 2026

• Can add qual string in header to --rename?

  marcelm/cutadapt#878 · Filter by author falsetry1514 opened on Apr 1, 2026

• How to handle reads with mixed primer sequences

  marcelm/cutadapt#875 · Filter by author tao-bioinfo opened on Mar 18, 2026

• read splitting concatameric read Nanopore

  marcelm/cutadapt#872 · Filter by author smartise opened on Feb 17, 2026
  2

• Cannot trim my primers in my reverse reads no matter what orientation I use.

  marcelm/cutadapt#869 · Filter by author kdbchau opened on Jan 6, 2026
  5

• Inconsistent Primer Removal in Different Amplicon Datasets Using Same cutadapt Command

  marcelm/cutadapt#867 · Filter by author rubadevis opened on Dec 2, 2025
  1

• binned quality scores in Illumina reads (paired ends)

  marcelm/cutadapt#865 · Filter by author l-gallucci opened on Nov 21, 2025
  5

• error with --rest-file or -r flags: AttributeError: 'LinkedMatch' object has no attribute 'rest'

  marcelm/cutadapt#856 · Filter by author clmattson opened on Aug 14, 2025
  1

• Sequences exceeding mismatch threshold not discarded as expected in Cutadapt 4.9

  marcelm/cutadapt#855 · Filter by author camilababo opened on Jul 25, 2025

• Adapter Cutting and Demultiplexing

  marcelm/cutadapt#854 · Filter by author gfill88 opened on Jul 8, 2025
  1

• Mixing file-based adapter and literal adapter in linked adapter

  marcelm/cutadapt#851 · Filter by author whatever60 opened on Jun 25, 2025
  2

• Demultiplexing from only read2 barcodes pushes all outputs to untrimmed

  marcelm/cutadapt#849 · Filter by author elliot-imler opened on Jun 17, 2025
  2

• How many barcodes can cutadapt handle at once?

  marcelm/cutadapt#848 · Filter by author zuoyichen opened on Jun 10, 2025
  2

• Demultiplexing and adapter/barcode trimming from PacBio amplicon reads

  marcelm/cutadapt#847 · Filter by author EndemicT opened on Jun 9, 2025
  4

• suggestions on primer+spacers using cutadapt

  marcelm/cutadapt#846 · Filter by author saharbagheri opened on Jun 5, 2025
  7

• Anchoring barcode file for demultiplexing throws an error

  marcelm/cutadapt#845 · Filter by author lchen3 opened on Jun 3, 2025
  1

• Exit after emitting X trimmed reads

  marcelm/cutadapt#844 · Filter by author sjaenick opened on May 30, 2025
  6

• how to clip a variable *end* 5' adapter?

  marcelm/cutadapt#841 · Filter by author yfarjoun opened on May 20, 2025
  5