Cutadapt¶

Description¶

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

You can check the installation documentation here.

sudo apt install cutadapt

Or possibly

sudo apt install python3-cutadapt

Verify the installation:

cudatapt --version

If you use conda, you can install cutadapt with:

conda install -c bioconda cutadapt

For the full list of options:

cutadapt -h

cutadapt -a <adapter-sequence> -o <output-file> <input-file>

For example, trimming an adapter (AGATCGGAAGAG in this case) from a fastq file will be:

cutadapt -a AGATCGGAAGAG -o output_reads.fastq input_reads.fastq

If you're working with paired-end reads, specify both input and output files:

cutadapt -a AGATCGGAAGAG -A AGATCGGAAGAG -o output_R1.fastq -p output_R2.fastq input_R1.fastq input_R2.fastq

You can use cutadapt to trim low-quality bases from the ends of reads ( in this example quality score < 20):

cutadapt -q 20 -o output_reads.fastq input_reads.fastq

And also to discard reads shorter than a selected value after trimming (in this example 30 nucleotides)

cutadapt -m 30 -o output_reads.fastq input_reads.fastq

Check out the full documentation on how to use cutadapt for all different types of adapters. Cutadapt can detect multiple adapter types:

Adapter Type	Command-line Option
Regular 3' adapter	`-a ADAPTER`
Regular 5' adapter	`-g ADAPTER`
Non-internal 3' adapter	`-a ADAPTERX`
Non-internal 5' adapter	`-g XADAPTER`
Anchored 3' adapter	`-a ADAPTER$`
Anchored 5' adapter	`-g ^ADAPTER`
5' or 3' (both possible)	`-b ADAPTER`
Linked adapter	`-a ADAPTER1...ADAPTER2 -g ADAPTER1...ADAPTER2`