vispa

ViSpA : Viral Spectrum Assembler   

Introduction

ViSpA implements a novel viral assembling and frequency estimation methods. This software uses a simple error correction, viral variants assembling based on maximum-bandwidth paths in weighted read graphs and frequency estimation via Expectation Maximization on all reads. Experiments show that ViSpA is better in quasispecies assembling than the state-of-the-art method of ShoRAH.

ViSpA source code

The software is written in Java, EM part is written in python, wrapper script is written in bash scripting language.

ViSpA can be downloaded here (vispa02.zip). See the readme.txt file for installation instructions.

Contacts

Alexander Zelikovsky

Irina Astrovskaya

Bassam Tork

Department of Computer Science

Georgia State University

34 Peachtree Str., 1443

Atlanta, GA 30303

Phone:  (404) 413 5730

Fax: (404) 413-5717

Email: alexz@cs.gsu.edu

web: http://www.cs.gsu.edu/~cscazz/

Department of Computer Science

Georgia State University

34 Peachtree Str., 1415

Atlanta, GA 30303

Email: iraa@cs.gsu.edu

Department of Computer Science

Georgia State University

34 Peachtree Str., 1415

Atlanta, GA 30303

Email: btork1@cs.gsu.edu

Related Publications

1. Astrovskaya, I., Tork, B., Mangul, S., Westbrooks, K., Mandoiu, I., Balfe, P., and Zelikovsky, A., Inferring Viral Spectrum from 454 Pyrosequencing Reads, 1st Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMBseqCCB2011), BMC Bioinformatics (to appear) pdf

(sup. materials)

2. Astrovskaya, Irina A., "Inferring Genomic Sequences" (2011). Computer Science Dissertations. Paper 59 (pdf). http://digitalarchive.gsu.edu/cs_diss/59
3. Westbrooks, K., Astrovskaya, I., Rendon, D. C., Khudyakov, Y., Berman, P., and Zelikovsky, A., HCV Quasispecies Assembly using Network Flows, Proc. of Fourth International Symposium on Bioinformatics Research and Applications (ISBRA 2008), Lecture Notes in Computer Science vol. 4983, pp. 159-170.

Related Presentations

1. Astrovskaya, I., Westbrooks, K., Tork, B., Mangul, S., Mandoiu, I., Balfe, P., and Zelikovsky, A., Inferring Viral Population from Ultra-Deep Sequencing Data, workshop on Computational Advances for Next Generation Sequencing (CANGS 2011) (invited talk), February 2011.
2. Astrovskaya, I., Westbrooks, and Zelikovsky, A., Reconstruction of HCV Quasispecies Haplotypes from 454 Life Science Reads, ISBRA 2010 (short abstract), May 2010.
3. Astrovskaya, I., Westbrooks, K., Tork, B., Mangul, S., Mandoiu, I., Balfe, P., and Zelikovsky, A., VISPA: Viral Spectrum Assembling Method, The 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS'11), February 2011, Best Poster Award.

This code may be freely used for all non-commercial purposes.
(c) Copyright, 2011 by Professor Alexander Zelikovsky
Department of Computer Science,
Georgia State University
Atlanta, GA 30303 (404) 413 5730
alexz@cs.gsu.edu http://www.cs.gsu.edu/~cscazz/Free via S

Call

Send SMS

Add to Skype

You'll need Skype CreditFree via Skype