---
name: "fastaq-sequence_trim"
section: "1"
platform: "linux"
package: "fastaq"
version: "3.17.0-9"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastaq-sequence_trim"
---

# fastaq-sequence\_trim(1)

Trim exact matches to a given string off the start of every sequence

## NAME

fastaq\_sequence\_trim - Trim exact matches to a given string off the start of every sequence

## DESCRIPTION

usage: fastaq\_sequence\_trim \[options\] \<infile\_1\> \<infile\_2\> \<outfile\_1\> \<outfile\_2\> \<trim\_seqs\>

Trims sequences off the start of all sequences in a pair of sequence files, whenever there is a perfect match. Only keeps a read pair if both reads of the pair are at least a minimum length after any trimming

### positional arguments:

- infile\_1

  Name of forward fasta/q file to be trimmed

- infile\_2

  Name of reverse fasta/q file to be trimmed

- outfile\_1

  Name of output forward fasta/q file

- outfile\_2

  Name of output reverse fasta/q file

- trim\_seqs

  Name of file of sequences to search for at the start of each input sequence

### options:

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

  show this help message and exit

- **--min\_length** INT

  Minimum length of output sequences \[50\]

- **--revcomp**

  Trim the end of each sequence if it matches the reverse complement. This option is intended for PCR primer trimming