Trimming Using Porechop

Oxford Nanopore adapter trimming, chimera splitting and barcode demultiplexing

Accepted formats: .fastq, .fq, .fastq.gz (Maximum size: 500 MB)

Porechop

Function

Porechop is a tool designed to identify and remove Oxford Nanopore adapter sequences from sequencing reads.

It can trim adapters from read ends, split reads containing internal adapters, and demultiplex reads according to barcode sequences.

Input Format

  • FASTQ (.fastq, .fq)
  • Compressed FASTQ (.fastq.gz)
  • Oxford Nanopore sequencing reads

Output Format

  • Trimmed FASTQ files
  • Optional barcode-specific FASTQ files
  • Adapter trimming statistics

Applications

  • Adapter removal
  • Chimera detection and splitting
  • Barcode demultiplexing
  • Nanopore preprocessing pipelines

Example Usage

porechop \
-i input.fastq.gz \
-o trimmed.fastq.gz

porechop \
-i input.fastq.gz \
-o trimmed.fastq.gz \
--threads 8

porechop \
-i input.fastq.gz \
-o trimmed.fastq.gz \
--discard_middle

Suggested Reading

Important Notes:
  • Designed exclusively for Oxford Nanopore data.
  • Can detect internal adapters and split reads.
  • Supports barcode demultiplexing.
  • Often used before alignment or assembly.
  • Porechop is no longer actively maintained; Porechop_ABI is a newer alternative.