MyPro includes the following software in a Virtual Box, please make sure you have accepted their license agreements if any.

Name	Download	Reference	Checkbox
Abyss 1.5.2	http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.5.2	(Simpson, et al., 2009)	□
Bio-Linux 8	http://environmentalomics.org/bio-linux-download/	(Field, et al., 2006)	□
CISA 1.3	http://sb.nhri.org.tw/CISA	(Lin and Liao, 2013)	□
Edena V3.131028	http://www.genomic.ch/edena.php	(Hernandez, et al., 2008)	□
FastQC 0.10.1	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/		□
Prokka 1.10	http://www.vicbioinformatics.com/software.prokka.shtml	(Seemann, 2014)	□
r2cat	http://bibiserv2.cebitec.uni-bielefeld.de/cgcat?viewType=download	(Husemann and Stoye, 2010)	□
SOAP2 2.21	http://soap.genomics.org.cn/soapaligner.html	(Li, et al., 2009)	□
SOAPdenovo 2.04	http://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2/bin/	(Luo, et al., 2012)	□
SPAdes 3.1.1	http://bioinf.spbau.ru/spades	(Bankevich, et al., 2012)	□
Tablet 1.14.04.10	http://ics.hutton.ac.uk/tablet/download-tablet/	(Milne, et al., 2013)	□
VelvetOptimiser 2.2.5	http://bioinformatics.net.au/software.velvetoptimiser.shtml	(Zerbino and Birney, 2008)	□

Please note that Abyss was made with maxk=128, Velvet was made with MAXKERLENGTH=127.

Installation of MyPro

Download Virtual Box

https://www.virtualbox.org/wiki/Downloads

Download MyPro.ova:

To download http://sb.nhri.org.tw/MyPro.ova (5.5GB) or http://sb.nhri.org.tw/MyPro.tar.gz (5.4GB)

Other information at: http://sourceforge.net/projects/sb2nhri/files/MyPro/

Open VirtualBox

File -> Import Appliance...

Select the file (MyPro.ova) to import

MyPro.ova

Or, directly double click on MyPro.ova

Please check the box of "Reinitialize the MAC address of all network cards"

Import

Open Terminal

Quick-start guide of MyPro

A. Pre-process

This script is used to trim, pair and sub-sample your raw reads. A total of 100X (paired) reads are generated. This process is strongly recommended; otherwise much computational time is required for genome assembly.

Command:

Preprocess.py -read1 S.gordonii_G9B_TTAGGC_L001_R1_001.fastq -read2 S.gordonii_G9B_TTAGGC_L001_R2_001.fastq -g 2200000

Preprocess.py -h for help.

B. AutoRun

This script is used to perform Assemble, Integrate and Annotate.

Command:

AutoRun.py G9B -read1 50X_R1.fastq -read2 50X_R2.fastq -evaluate -p '--prefix G9B --genus Streptococcus --species gordonii --strain G9B --addgenes --locustag AA01'

AutoRun.py -h, Assemble.py -h, Integrate.py -h and Annotate.py -h for help.

C. Post-assemble

This script is to (1) merge your ordered contigs if they are overlapped and (2) fill gaps with the contigs of local assembling.

(Optional) To use r2cat.jar for ordering your contigs against a related reference genome. You can Export contigs order (FASTA) and Export unmatched contigs (FASTA) separately.

Command:

Postassemble.py -o cisa.ordered.fa -u unmatched.fa -read1 ../50X_R1.fastq -read2 ../50X_R2.fastq

No reference genome:

Postassemble.py -u cisa.ctg.fa -read1 ../50X_R1.fastq -read2 ../50X_R2.fastq

Postassemble.py -h for help.

MyPro has been published in Journal of Microbiologic Methods (http://www.sciencedirect.com/science/article/pii/S0167701215001207). Please download http://sourceforge.net/projects/sb2nhri/files/MyPro/Supplementary%20Information.pdf/download for details.