Cutadapt

Marcel Martin |

Cutadapt

Omics

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About
API Example

Step 1: Upload your data

Upload Read-1 FASTQ File

Drag your file(s) or upload

Your file can be in the following formats:fastq, fastq.gz

FASTQ format is text based, human readable, file that stores nucleotide base sequences with a quality(Phred) score for each base.

Don’t have a file?

Use our demo data to run

Use Demo Data

Upload Read-2 FASTQ File

Drag your file(s) or upload

Your file can be in the following formats:fastq, fastq.gz

FASTQ format is text based, human readable, file that stores nucleotide base sequences with a quality(Phred) score for each base. If the experimental setup is paired-end sequencing, R2 file must be uploaded as well.

Don’t have a file?

Use our demo data to run

Use Demo Data

Upload Forward Adapter File

Drag your file(s) or upload

Your file can be in the following formats:fasta,

Adapter(s) must be provided in .fasta file format. You can add multiple adapter sequences by using same structure below. Example: >adapter1 GTTCCAATCTCAAATGGC >adapter2 ATTCGGGTCTCAAATGGC

Don’t have a file?

Use our demo data to run

Use Demo Data

View example data

Upload Reverse Adapter File

Drag your file(s) or upload

Your file can be in the following formats:fasta,

Adapter(s) must be provided in .fasta file format. You can add multiple adapter sequences by using same structure below. If your experimental setup is paired-end sequencing, you need to add reverse adapter file as well. Example: >adapter1 GTTCCAATCTCAAATGGC >adapter2 ATTCGGGTCTCAAATGGC

Don’t have a file?

Use our demo data to run

Use Demo Data

View example data

Step 2: Set Parameters

Library Output

Paired-End

Step 3: Complete run profile

Job name - Optional

Data quality can be important for downstream analysis (e.g. alignment) and data cleaning is one of the most important steps to improve data quality. This app eliminates unnecessary reads from your sequence (e.g. adapters, primers, Poly-A tails). Inputs are FASTQ reads and adapters sequences. Output is an info table generated by the Cudatapt algorithm. Based on Cutadapt version v4.1.

Example Use Case: Remove unwanted 3' adapters from the FASTQ sequence

Limitation: Currently, only 3' adapters are accepted

Citation:

Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17 (1), pp. 10-12. doi: https://doi.org/10.14806/ej.17.1.200

Released:
Nov-23-2022

Previous Job Parameters

Your previous job parameters will show up here
so you can keep track of your jobs

Results

Parameters