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NPBSS 2018/03/01 ver1.0.0 ICI/LIFT, China

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System Requirements

Runtime Environment Requirements

Octave 4.2.1 or later

Software Requirements

The NPBSS is supported on the following operating systems

Windows 7 Windows 10

Hardware Requirements/Recommendations

Intel Core i3 2100 or later for Windows Color display capable of 1024 X 768 pixel resolution

Memory Requirements/Recommendations

NPBSS requires approximately 5 G of available disk space on the drive or partition.

NPBSS requires a minimum of 2G of RAM for simulating PacBio CLR reads.

User's Guide

Input Genome File Requirements

Input genome file is *.fasta or *.txt and input sequences require FASTA format, e.g.

Genome_name AAACACTTGACATGTTCGTCGCGACTCTAAGAGATTAGAGTTTTCGGTTCGGCCGGACGAAACAC...

Execute Step

Step 1: Install Octave (https://ftp.gnu.org/gnu/octave/windows/octave-4.2.1-w64-installer.exe). Step 2: Download NPBSS_Octave zip file (https://github.com/NWPU-903PR/NPBSS_Octave/archive/master.zip) and unzip. Step 3: Open Octave and change 'File Broswer' to the 'NPBSS_Octave-master' folder. Step 4: Type in NPBSS('ecoliGenome.fa','-n 100') in the Command Window. Step 5: Press 'ENTER' key to run. Step 6: The final simulated sequences files can be found in the 'NPBSS_Octave' directory.

Test: The scatter plot of read length and average base quality per read can be run by: qv_average_each_read('simulated.fq')

Copyright Notice

Software, documentation and related materials: Copyright (c) 2018-2020 Institute of Control & Information(ICI), Northwestern Polytechnical University,China Key Laboratory of Information Fusion Technology(LIFT), Ministry of Education, China All rights reserved.