Readjoiner

Readjoiner is a sequence assembler based on the assembly string graph framework (Myers 2005). It is faster and uses less memory than previous string graph-based assemblers.

Download

Readjoiner 1.2 is available in GenomeTools 1.4.2.

Latest GenomeTools Release:

• binaries: http://genometools.org/pub/binary_distributions/
• source code: http://genometools.org/pub/genometools-1.4.2.tar.gz

Development Version (possibly unstable):

• binaries (Linux): http://genometools.org/pub/nightly_builds/
• source code: http://genometools.org/pub/genometools-unstable.tar.gz

Changelog

v 1.2

• readjoiner overlap able to use multiple threads
• several performance improvements
• support for input in FASTQ format

v 1.1

• complete support of variable length read sets: prefilter now automatically recognizes variable length files (the -varlen option was dropped) and the overlap and assembly tools now correctly handle variable length datasets
• prefilter accepts multiple filenames as input
• some compilation issues were fixed (the make option "errorcheck=no" might still be necessary when compiling on a PC-Solaris machine)

v 1.0

• initial release

Usage

Download the pre-compiled 64-bit binary for your platform (Linux or Mac). Alternatively you may want to download the source code and compile it using the provided Makefile (for more information see the INSTALL file in the main directory of the sources).

The Readjoiner pipeline consists of the following tools:

• prefilter
• overlap
• assembly

The tools are integrated in the GenomeTools binary gt and can be run using the command:

gt readjoiner <toolname> [-options]

Use the option

-help

for more information about a tool.
The Readjoiner user manual provides more information.

References

G. Gonnella, S. Kurtz:
Readjoiner: a fast and memory efficient string graph-based sequence assembler.
BMC Bioinformatics, 13:82 (2012)

E.W. Myers:
The fragment assembly string graph.
Bioinformatics, 21 Suppl 2:79–85(2005)