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





Abyss 1.5.2

(Simpson, et al., 2009)

Bio-Linux 8

(Field, et al., 2006)

CISA 1.3

(Lin and Liao, 2013)

Edena V3.131028

(Hernandez, et al., 2008)

FastQC 0.10.1


Prokka 1.10

(Seemann, 2014)


(Husemann and Stoye, 2010)

SOAP2 2.21

(Li, et al., 2009)

SOAPdenovo 2.04

(Luo, et al., 2012)

SPAdes 3.1.1

(Bankevich, et al., 2012)


(Milne, et al., 2013)

VelvetOptimiser 2.2.5

(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


Download MyPro.ova:

To download (5.5GB) or (5.4GB)


Other information at:


Open VirtualBox

File -> Import Appliance...

Select the file (MyPro.ova) to import



Or, directly double click on MyPro.ova


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


Open Terminal

描述: 描述: C:\Users\Jade\AppData\Local\Temp\enhtmlclip\Image(105).png

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: -read1 S.gordonii_G9B_TTAGGC_L001_R1_001.fastq -read2 S.gordonii_G9B_TTAGGC_L001_R2_001.fastq -g 2200000 -h for help.


B. AutoRun

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


Command: G9B -read1 50X_R1.fastq -read2 50X_R2.fastq -evaluate -p '--prefix G9B --genus Streptococcus --species gordonii --strain G9B --addgenes --locustag AA01' -h, -h, -h and -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: -o cisa.ordered.fa -u unmatched.fa -read1 ../50X_R1.fastq -read2 ../50X_R2.fastq


No reference genome: -u cisa.ctg.fa -read1 ../50X_R1.fastq -read2 ../50X_R2.fastq -h for help.


MyPro has been published in Journal of Microbiologic Methods ( Please download for details.