marcelm/cutadapt

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Cutadapt removes adapter sequences from sequencing reads

Stars: 587
Forks: 144
Open beginner issues: 0
Indexed issues: 105
Avg merge: 2h 37m
Merged PRs (30d): 1

Dominant language: Python
License: MIT
Last GitHub push: Sep 14, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

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105 open issues indexed

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) Open

Difficulty 4/5 3-5 days Newbie friendliness 65/100

marcelm/cutadapt#892 · Opened Sep 3, 2026
documentation for using info-file with linked adapters Open

Difficulty 1/5 Under an hour Newbie friendliness 85/100

marcelm/cutadapt#890 · Opened Aug 15, 2026
Error when combining multiple 5' adapter search with -g file: and ;rightmost Open

Difficulty 3/5 1-2 days Newbie friendliness 65/100

marcelm/cutadapt#889 · Opened Jul 31, 2026
Question: Combinatorial multiplexing on single reads Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

marcelm/cutadapt#887 · 1 comment · Opened Jun 30, 2026
Questions about parameters -a and -O Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

marcelm/cutadapt#884 · Opened May 9, 2026
Some polyGs at the end of the sequences are not removed Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

marcelm/cutadapt#883 · Opened May 6, 2026
Feature request: empirical sequencing-error-rate estimation Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

marcelm/cutadapt#881 · Opened May 4, 2026
Adapter trimming and demultiplexing Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

marcelm/cutadapt#880 · Opened Apr 30, 2026
Can add qual string in header to --rename? Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

marcelm/cutadapt#878 · Opened Apr 1, 2026
How to handle reads with mixed primer sequences Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

marcelm/cutadapt#875 · Opened Mar 18, 2026
read splitting concatameric read Nanopore Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

marcelm/cutadapt#872 · 2 comments · Opened Feb 17, 2026
Cannot trim my primers in my reverse reads no matter what orientation I use. Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

marcelm/cutadapt#869 · 5 comments · Opened Jan 6, 2026
Inconsistent Primer Removal in Different Amplicon Datasets Using Same cutadapt Command Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

marcelm/cutadapt#867 · 1 comment · Opened Dec 2, 2025
binned quality scores in Illumina reads (paired ends) Open

Difficulty 4/5 3-5 days Newbie friendliness 32/100

marcelm/cutadapt#865 · 5 comments · Opened Nov 21, 2025
error with --rest-file or -r flags: AttributeError: 'LinkedMatch' object has no attribute 'rest' Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

marcelm/cutadapt#856 · 1 comment · Opened Aug 14, 2025
Sequences exceeding mismatch threshold not discarded as expected in Cutadapt 4.9 Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

marcelm/cutadapt#855 · Opened Jul 25, 2025
Adapter Cutting and Demultiplexing Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

marcelm/cutadapt#854 · 1 comment · Opened Jul 8, 2025
Mixing file-based adapter and literal adapter in linked adapter Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

marcelm/cutadapt#851 · 2 comments · Opened Jun 25, 2025
Demultiplexing from only read2 barcodes pushes all outputs to untrimmed Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

marcelm/cutadapt#849 · 2 comments · Opened Jun 17, 2025
How many barcodes can cutadapt handle at once? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

marcelm/cutadapt#848 · 2 comments · Opened Jun 10, 2025
Demultiplexing and adapter/barcode trimming from PacBio amplicon reads Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

marcelm/cutadapt#847 · 4 comments · Opened Jun 9, 2025
suggestions on primer+spacers using cutadapt Open

Difficulty 4/5 3-5 days Newbie friendliness 15/100

marcelm/cutadapt#846 · 7 comments · Opened Jun 5, 2025
Anchoring barcode file for demultiplexing throws an error Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

marcelm/cutadapt#845 · 1 comment · Opened Jun 3, 2025
Exit after emitting X trimmed reads Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

marcelm/cutadapt#844 · 6 comments · Opened May 30, 2025
how to clip a variable *end* 5' adapter? Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

marcelm/cutadapt#841 · 5 comments · Opened May 20, 2025
Incomplete Adapter Trimming with Cutadapt 5.0 Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

marcelm/cutadapt#839 · 3 comments · Opened May 1, 2025
Amplicon primer trimming and Demultiplexing Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

marcelm/cutadapt#837 · 4 comments · Opened Apr 22, 2025
Question: How to trim multiple overhang adapter sequences and primers from paired-end Fastq files Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

marcelm/cutadapt#836 · 2 comments · Opened Apr 19, 2025
Issue about Read Count Differences When Using -e and --overlap Options Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

marcelm/cutadapt#835 · 1 comment · Opened Apr 7, 2025
Problems when running highly parallel and writing GZ files Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

marcelm/cutadapt#833 · 3 comments · Opened Mar 18, 2025
Issue with Mismatch Settings in Cutadapt for Demultiplexing Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

marcelm/cutadapt#832 · 2 comments · Opened Feb 17, 2025
Removal of both 5' and 3' adaptors in paired-end reads Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

marcelm/cutadapt#831 · 2 comments · Opened Feb 5, 2025
Warn if adapters cannot be indexed Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

marcelm/cutadapt#823 · Opened Dec 5, 2024
Feature request: control info-file column separator Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

marcelm/cutadapt#816 · 5 comments · Opened Nov 6, 2024
I have 5' and 3' adapter sequences for the paired read sequencing data? how should I remove them Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

marcelm/cutadapt#813 · 15 comments · Opened Oct 14, 2024
Trimming reads generated by the template switching RT Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

marcelm/cutadapt#810 · 1 comment · Opened Sep 24, 2024
[Question] linked adapters from Fasta file and discarding untrimmed pairs Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

marcelm/cutadapt#806 · 1 comment · Opened Sep 6, 2024
Suggestion: filter mode for polyA Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

marcelm/cutadapt#805 · 2 comments · Opened Aug 29, 2024
Should I use -a or -g when demultiplexing ONT reads with dual barcodes? Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

marcelm/cutadapt#799 · 4 comments · Opened Aug 9, 2024
Primer sequence trimming. Cutadapt does not cut all of them Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

marcelm/cutadapt#798 · 1 comment · Opened Aug 8, 2024
Heterogeneity Spacers and Primers Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

marcelm/cutadapt#792 · 5 comments · Opened Jul 2, 2024
Adapter matches in the middle of a read masked with N Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

marcelm/cutadapt#787 · 2 comments · Opened May 21, 2024
cutadapt: error: cutadapt not able to trim the desired adapto Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

marcelm/cutadapt#785 · 3 comments · Opened May 11, 2024
"OverflowError: FASTA/FASTQ record does not fit into buffer" when trimming ONT reads Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

marcelm/cutadapt#783 · 7 comments · Opened May 1, 2024
Remove the "Incomplete adapter sequence" warning Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

marcelm/cutadapt#780 · Opened Apr 23, 2024
Ensuring to find the correct file after Demultiplexing my 16S amplicon raw dataset with combinatorial dual indexes cutadapt command Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

marcelm/cutadapt#776 · 5 comments · Opened Apr 16, 2024
Feature request: Support for multiple FastQ pairs Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

marcelm/cutadapt#775 · Opened Mar 27, 2024
Vectorize alignment algorithm for x86-64 Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

marcelm/cutadapt#768 · 1 comment · Opened Mar 15, 2024
Output of demultiplexing mixed oriented reads Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

marcelm/cutadapt#764 · 5 comments · Opened Mar 1, 2024
When demultiplexing, report contains irrelevant line Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

marcelm/cutadapt#760 · Opened Feb 2, 2024

marcelm/cutadapt

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