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.

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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

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