Phusion2 is a pipeline for de novo genome assembly using NGS data. It is based upon a strategy called read clustering. Starting with kmer frequency analysis, this allows for a reasonable selection of the kmer sizes. K-tuples from raw reads are merged and sorted into a table so that multiple occurring kmer words shared by different reads can be linked. A relation matrix is used to record the shared kmer words among all the reads. Setting a minimum threshold of shared k-tuples, the whole set of reads can then be clustered into groups using kmer sharing information in the relational matrix. After obtaining small read clusters with a controllable size, a local assembler can be used to produce contigs.

The Phusion2 pipeline was used in assembling a number of genomes, such as Gorilla, Zebrafish, Tasmanian Devil, Bamboo and Miscanthus, etc.

Learn and Support

Contact the developers for more technical details and instructions.

License and Citation

Copyright (C) 2008 - 2015 Genome Research Ltd.

Author: Zemin Ning

Phusion2 is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the
Free Software Foundation, either version 3 of the License, or (at your
option) any later version.

This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program. If not, see <>.


For more information, please contact: Zemin Ning ( ).


Sanger Contributors


  • The phusion assembler.

    Mullikin JC and Ning Z

    Genome research 2003;13;1;81-90

  • Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer.

    Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ et al.

    Cell 2012;148;4;780-91

  • The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla).

    Peng Z, Lu Y, Li L, Zhao Q, Feng Q et al.

    Nature genetics 2013;45;4;456-61, 461e1-2

  • The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation.

    Wang Y, Lu Y, Zhang Y, Ning Z, Li Y et al.

    Nature genetics 2015;47;6;625-31

Tool Type