---
name: "AssemblePairs.py"
section: "1"
platform: "linux"
package: "presto"
version: "0.7.2-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/AssemblePairs.py"
---

# AssemblePairs.py(1)

Assembles paired-end reads into a single sequence

## NAME

AssemblePairs.py - Assembles paired-end reads into a single sequence

## DESCRIPTION

usage: AssemblePairs.py \[--version\] \[-h\]  ...

Assembles paired-end reads into a single sequence

### help:

- **--version**

  show program's version number and exit

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

  show this help message and exit

### subcommands:

-

  Assembly method

- align

  Assemble pairs by aligning ends.

- join

  Assemble pairs by concatenating ends.

-

  reference

-

  Assemble pairs by aligning reads against a reference database.

-

  sequential

-

  Assemble pairs by first attempting de novo assembly, then reference guided assembly.

### output files:

-

  assemble-pass

-

  successfully assembled reads.

-

  assemble-fail

-

  raw reads failing paired-end assembly.

### output annotation fields:

-

  \<user defined\>

-

  annotation fields specified by the **--1f** or **--2f** arguments.

## AUTHOR

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