---
name: "porechop"
section: "1"
platform: "linux"
package: "porechop"
version: "0.2.4+dfsg-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/porechop"
---

# porechop(1)

adapter trimmer for Oxford Nanopore reads

## NAME

porechop - adapter trimmer for Oxford Nanopore reads

## SYNOPSIS

**porechop** \[-h\] **-i** INPUT \[-o OUTPUT\] \[--format {auto,fasta,fastq,fasta.gz,fastq.gz}\] \[-v VERBOSITY\] \[-t THREADS\] \[--version\] \[-b BARCODE\_DIR\] \[--barcode\_threshold BARCODE\_THRESHOLD\] \[--barcode\_diff BARCODE\_DIFF\] \[--require\_two\_barcodes\] \[--untrimmed\] \[--discard\_unassigned\] \[--adapter\_threshold ADAPTER\_THRESHOLD\] \[--check\_reads CHECK\_READS\] \[--scoring\_scheme SCORING\_SCHEME\] \[--end\_size END\_SIZE\] \[--min\_trim\_size MIN\_TRIM\_SIZE\] \[--extra\_end\_trim EXTRA\_END\_TRIM\] \[--end\_threshold END\_THRESHOLD\] \[--no\_split\] \[--discard\_middle\] \[--middle\_threshold MIDDLE\_THRESHOLD\] \[--extra\_middle\_trim\_good\_side EXTRA\_MIDDLE\_TRIM\_GOOD\_SIDE\] \[--extra\_middle\_trim\_bad\_side EXTRA\_MIDDLE\_TRIM\_BAD\_SIDE\] \[--min\_split\_read\_size MIN\_SPLIT\_READ\_SIZE\]

## DESCRIPTION

Porechop: a tool for finding adapters in Oxford Nanopore reads, trimming them from the ends and splitting reads with internal adapters

## OPTIONS

### optional arguments:

- **-h**, **--help**

  show this help message and exit

### Main options:

- **-i** INPUT, **--input** INPUT

  FASTA/FASTQ of input reads or a directory which will be recursively searched for FASTQ files (required)

- **-o** OUTPUT, **--output** OUTPUT

  Filename for FASTA or FASTQ of trimmed reads (if not set, trimmed reads will be printed to stdout)

- **--format** {auto,fasta,fastq,fasta.gz,fastq.gz}

  Output format for the reads - if auto, the format will be chosen based on the output filename or the input read format (default: auto)

- **-v** VERBOSITY, **--verbosity** VERBOSITY

  Level of progress information: 0 = none, 1 = some, 2 = lots, 3 = full - output will go to stdout if reads are saved to a file and stderr if reads are printed to stdout (default: 1)

- **-t** THREADS, **--threads** THREADS

  Number of threads to use for adapter alignment (default: 4)

- **--version**

  show program's version number and exit

### Barcode binning settings:

-

  Control the binning of reads based on barcodes (i.e. barcode demultiplexing)

- **-b** BARCODE\_DIR, **--barcode\_dir** BARCODE\_DIR

  Reads will be binned based on their barcode and saved to separate files in this directory (incompatible with **--output**)

- **--barcode\_threshold** BARCODE\_THRESHOLD

  A read must have at least this percent identity to a barcode to be binned (default: 75.0)

- **--barcode\_diff** BARCODE\_DIFF

  If the difference between a read's best barcode identity and its second-best barcode identity is less than this value, it will not be put in a barcode bin (to exclude cases which are too close to call) (default: 5.0)

- **--require\_two\_barcodes**

  Reads will only be put in barcode bins if they have a strong match for the barcode on both their start and end (default: a read can be binned with a match at its start or end)

- **--untrimmed**

  Bin reads but do not trim them (appropriate if reads are to be used with Nanopolish) (default: trim the reads)

- **--discard\_unassigned**

  Discard unassigned reads (instead of creating a "none" bin) (default: False)

### Adapter search settings:

-

  Control how the program determines which adapter sets are present

- **--adapter\_threshold** ADAPTER\_THRESHOLD

  An adapter set has to have at least this percent identity to be labelled as present and trimmed off (0 to 100) (default: 90.0)

- **--check\_reads** CHECK\_READS

  This many reads will be aligned to all possible adapters to determine which adapter sets are present (default: 10000)

- **--scoring\_scheme** SCORING\_SCHEME

  Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend (default: 3,-6,-5,-2)

### End adapter settings:

-

  Control the trimming of adapters from read ends

- **--end\_size** END\_SIZE

  The number of base pairs at each end of the read which will be searched for adapter sequences (default: 150)

- **--min\_trim\_size** MIN\_TRIM\_SIZE

  Adapter alignments smaller than this will be ignored (default: 4)

- **--extra\_end\_trim** EXTRA\_END\_TRIM

  This many additional bases will be removed next to adapters found at the ends of reads (default: 2)

- **--end\_threshold** END\_THRESHOLD

  Adapters at the ends of reads must have at least this percent identity to be removed (0 to 100) (default: 75.0)

### Middle adapter settings:

-

  Control the splitting of read from middle adapters

- **--no\_split**

  Skip splitting reads based on middle adapters (default: split reads when an adapter is found in the middle)

- **--discard\_middle**

  Reads with middle adapters will be discarded (default: reads with middle adapters are split) (this option is on by default when outputting reads into barcode bins)

- **--middle\_threshold** MIDDLE\_THRESHOLD

  Adapters in the middle of reads must have at least this percent identity to be found (0 to 100) (default: 85.0)

- **--extra\_middle\_trim\_good\_side** EXTRA\_MIDDLE\_TRIM\_GOOD\_SIDE

  This many additional bases will be removed next to middle adapters on their "good" side (default: 10)

- **--extra\_middle\_trim\_bad\_side** EXTRA\_MIDDLE\_TRIM\_BAD\_SIDE

  This many additional bases will be removed next to middle adapters on their "bad" side (default: 100)

- **--min\_split\_read\_size** MIN\_SPLIT\_READ\_SIZE

  Post-split read pieces smaller than this many base pairs will not be outputted (default: 1000)

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.