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

# fastaq-capillary\_to\_pairs(1)

Converts file of capillary reads to paired and unpaired files

## NAME

fastaq\_capillary\_to\_pairs - Converts file of capillary reads to paired and unpaired files

## DESCRIPTION

usage: fastaq\_capillary\_to\_pairs \<infile\> \<outfiles prefix\>

Given a file of capillary reads, makes an interleaved file of read pairs (where more than read from same ligation, takes the longest read) and a file of unpaired reads. Replaces the .p1k/.q1k part of read names to denote fwd/rev reads with */1* and */2*

### positional arguments:

- infile

  Name of input fasta/q file

- outfiles prefix

  Prefix of output files

### options:

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

  show this help message and exit