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.
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.
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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
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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 <http://www.gnu.org/licenses/>.
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For more information, please contact: Zemin Ning ( email@example.com ).