Launch the workflow at the Latch console

Remove adapter sequences, primers, poly-A tails and other types of unwanted sequence using cutadapt | Pertinent information obtained from cutadapt original documentation

About

Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter single-end and paired-end reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Cutadapt can also demultiplex your reads.

Case use

Analyzing next generation sequencing data requires the removal of unwanted adapters from the raw reads. These include:

3’ sequencing adapter from small-RNA sequencing

Primer sequence in amplicon reads

Poly-A tails use in pulling out RNA from your sample

Cutadapt workflow uses the cutadapt program to remove adapter or primer sequences in an error-tolerant way

Basic usage:

You can use cutadapt on the single end read mode:

To use cutadapt, you will need to supply:

Trimming regular adapters

Supply the relevant adapter i.e 3’ or 5’ adapter e.g AACCGGTT and checkout the related trimming adapter function

Other adapters

You can also trim other adapters by checking relevant boxes

• Non-internal 3’ adapter

• Non-internal 5’ adapter

• Anchored 3’ adapter

• Anchored 5’ adapter

Additionally, you will need to input the FASTA or FASTQ file and select an output directory for your files, then let the console do the rest

The workflow has been configured to generate:

• cutadapt_info_file.fasta: This files contains detailed information about where adapters were found in the read
  

• cutadapt_report.json: This contains the full report after it has finished processing the reads.
  

• SE_Trim.fasta: This file contains the results of trimming the single end read
  

• untrimmed_file.fasta: File contains results of the first read when the processed pair was not trimmed
  

Paired end reads

Cutadapt workflow can also process paired end reads. This will require that you supply read 1 and read 2 as input files

In paired-end mode, Cutadapt checks whether the input files are properly paired.

An error is raised if one of the files contains more reads than the other or if the read names in the two files do not match.

> IMPORTANT NOTE: The info file will only contain information only from the first read.<br>

In Paired end mode, you will access the following files:

• cutadapt_report.json: This contains the full report after it has finished processing the reads.
  

• PE_trim_1.fasta: This file contains the results of trimming read 1
  

• PE_trim_2.fasta: This file contains the results of trimming read 2
  

• untrimmed_file.fasta: File contains results of the first read in a pair when the processed pair was not trimmed
  

• untrimmed__paired_file.fasta: File contains results of the first read in a pair when the processed pair was not trimmed