---
name: "gt-readjoiner-assembly"
section: "1"
platform: "linux"
package: "genometools"
version: "1.6.5+ds-2.2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gt-readjoiner-assembly"
---

# gt-readjoiner-assembly(1)

Construct string graph and output contigs.

## NAME

gt-readjoiner-assembly - Construct string graph and output contigs.

## SYNOPSIS

**gt readjoiner assembly** \[option ...\]

## DESCRIPTION

- **-readset** \[*string*\]

  specify the readset name (default: undefined)

- **-spmfiles** \[*value*\]

  number of SPM files to read this must be equal to the value of -j for the overlap phase (default: 1)

- **-l** \[*value*\]

  specify the minimum SPM length (default: 0)

- **-depthcutoff** \[*value*\]

  specify the minimal number of nodes in a contig (default: 3)

- **-lengthcutoff** \[*value*\]

  specify the minimal length of a contig (default: 100)

- **-errors** \[*yes\|no*\]

  search graph features which may originate from sequencing errors and remove them (default: no)

- **-bubble** \[*value*\]

  number of rounds of p-bubble removal to perform (default: 3)

- **-deadend** \[*value*\]

  number of rounds of dead end removal to perform a dead end (default: 10)

- **-deadend-depth** \[*value*\]

  specify the maximal depth of a path to an end-vertex by which the path shall be considered a dead end (default: 10)

- **-v** \[*yes\|no*\]

  be verbose (default: no)

- **-q** \[*yes\|no*\]

  suppress standard output messages (default: no)

- **-help**

  display help for basic options and exit

- **-help+**

  display help for all options and exit

- **-version**

  display version information and exit

## REPORTING BUGS

Report bugs to https://github.com/genometools/genometools/issues.