About the Software

Authors: Jixin Deng and Kim C. Worley

Atlas-Link links and orients genome sequence contigs quickly and accurately using mate-pair information. Atlas-Link can take advantage of unused mate-pair data from a WGS genome assembly or additional sequence data from different sequencing technologies or more recent sequence production. Atlas-Link currently supports Illumina, SOLiD, 454, and Sanger sequencing technologies.

Atlas-Link can operate on a de novo genome assembly provided as a set of contigs with mapping information for the sequence reads. Alternatively, Atlas-Link can superscaffold an existing genome assembly when provided with the .agp file of the assembly. In this iterative improvement mode, Atlas-Link retains the scaffolding information that exists from the input genome and incorporates the additional scaffolding information in a revised genome scaffold. The software implements a greedy algorithm and uses graph theory.

The Atlas-Link software takes a file describing the library information for the mate pair data, a file describing the read alignment information based on the TIGR Assembler’s adaptation of the GDE alignment format (, and a configuration file in xml format, and an optional .agp file (

Example files are included in the download package.

System Requirements and Installation


  • Navigate to the Atlas-Link download directory in a terminal window

  • Run: perl Makefile.PL PREFIX=(your current working folder)

  • Run: make

  • Run: make install


Copyright © Baylor College of Medicine Human Genome Sequencing Center. All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  • Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

  • Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.


By downloading this software you explicitly agree to the license terms above.

Current release: Atlas-Link

Version 0.01 (10-18-2010):


For additional information, contact Kim Worley ( or Jixin Deng (