SMIS

SMIS

SMIS

Overview

SMIS ( Single Molecular Integrative Scaffolding ): an assembly pipeline to improve genome scaffolding using Oxford Nanopore or PacBio long reads.

Learn and Support

# Long reads are shreded into small segments (1000bp or 2000bp) to make fake mate pairs

# Genome scaffolder spinner is used for scaffolding

# Say if you have an existing assembly from Illumina reads target.fasta and ONT long reads: ontreads.fastq Usage:

./smis_pipeline -nodes 20 -score 50 -len 2000 -step 200 -contig 3000 -edge 5 <ONT_fasta/q_file> <assembly_fasta/q_file> <scaffold-output.fasta_file>

nodes - number of CPUs requested;

score - minimum smith-waterman alignment score to report a hit;

len - length of fregments of fake mate pairs;

step - jump length to cut out fregments contig - minimum contig length to be included for scaffolding;

edge - minimum number of edges to confirm a merge

======== Install: ========

gunzip smis.tar.gz

tar xvf smis.tar

make Note:

You need to type the full path in order to make it work.

License and Citation

Copyright (C) 2014 - 2015 Genome Research Ltd.

Author: Zemin Ning


SMIS 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/>.

Contact

For more information, please contact: Zemin Ning ( zn1@sanger.ac.uk ).

Authors

Sanger Contributors

Tool Type