Cross_genome

Cross_genome is a package to build up genome assembly scaffolds using cross-species synteny.

Cross_genome is a package to build up genome assembly scaffolds using cross-species synteny.

Downloads

Download:

http://sourceforge.net/projects/phusion2/files/cross_genome/

Further information

Learn and support

./cross_genome -gap 20000 -nodes 20 -score 100 <ref_fasta/q_file> <assembly_fasta/q_file> <merged.fasta_file>

./cross_genome -gap 20000 -nodes 20 -score 100 ref_fasta target_fasta merged.fasta

gap: maximum gap size allowed to join the two contigs
node: number of CPU threads
score: Smith-waterman score

Note: using larger gap size can increase scaffold size, but sometimes, it
also brings errors.

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Install:
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gunzip cross_genome.tar.gz
tar xvf cross_genome.tar
make

License and Citation

Copyright (C) 2009 – 2015 Genome Research Ltd.

Author: Zemin Ning

Cross_genome 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/>.