B-SOLANA

Function

B-SOLANA provides a fast and accurate all-in-one approach including alignment and methylation calling of two-base encoding (“colorspace”) bisulfite sequencing data.

The publication of B-SOLANA in Bioinformatics can be found here

Our review about primary data analysis in BS-Seq can be found here

The development of B-SOLANA was partly funded by: The German Ministry of Education and Research (BMBF); the National Genome Research Network (NGFN); the Deutsche Forschungsgemeinschaft (DFG) Cluster of Excellence ‘Inflammation at Interfaces’; the EU Seventh Framework Programme (FP7/2007-2013, grant number 262055, ESGI).

Coding language

Python (http://www.python.org/)

Requirements

• Minimum hardware requirements: 4 processors, 8GB RAM.
• Operating System requirements: B-SOLANA has been developed for Linux/UNIX. We have tested the software on a 64-bit version of Linux, Ubuntu Linux 10.04. To download Ubuntu and for installation instructions go to: http://www.ubuntu.com
• A functional version of the short read aligner Bowtie (version 0.12.7 or later) http://bowtie-bio.sourceforge.net/index.shtml
• A functional version of SAMtools http://samtools.sourceforge.net/

Code released

This program 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. See http://www.gnu.org/licenses/

Initial Contact

Benjamin Kreck (send mail to: b dot kreck at ikmb dot uni-kiel dot de)

Introduction

B-SOLANA performs sequence alignment and methylation calling for two-base encoding (colorspace) bisulfite sequencing. It is based on the established short read aligner Bowtie (Langmead, 2009) and SAMtools, utilities for manipulating alignments (Li, 2009). B-SOLANA is divided into four individual steps: 1. Indexing 1. Mapping 1. Determination of best alignment 1. Methylation calling

There is a script, bsolana run, which is a composition of all steps mentioned above.

Installation

• Download the current version of B-SOLANA at Downloads and uncompress in a directory of your choice
• Ensure that the first line of the B-SOLANA script includes the path of your current Python version (check by „which python“ for Linux systems).
• Download and install short read aligner Bowtie (version 0.12.7 or later) available at: http://bowtie-bio.sourceforge.net/index.shtml
• Download and install SAMtools (utilities for manipulating alignments in the SAM/BAM format), preferably version 0.1.8 or later, available at: http://samtools.sourceforge.net/
• Fasta files of reference genomes are available for download at various websites, among them Ensembl (http://www.ensembl.org/info/data/ftp/index.html/) and NCBI (ftp://ftp.ncbi.nih.gov/genomes/)

See the manual of B-SOLANA at Downloads for further information.

Test data

We generated a test data set of 1 000 000 sequences (read length: 50 bp, SOLiD version 4).

Download the B-SOLANA software compressed file at Downloads and uncompress in a directory of your choice. Download the fasta file of hg19 (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/). Change to the directory of B-SOLANA executable files and start the analysis:

• [bash]$ bsolana run -ref <path of fasta reference file> -bowtie <Path of executable bowtie version> -samtools <Path of executable SAMtools version> -work ./test/results/ -csfasta ./test/sequences/test_F3.csfasta -qual ./test/sequences/test_F3.qual -thread 4 -name test

Results will be located in the subfolder .../test/results of the B-SOLANA home directory.

References

• Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9

• Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25

Changelog

• 14-11-2011: Version 1.0 released

  • Fixed a bug with the indexing of the reference genome
  • Speed up the runtime of bsolana bemap

• 26-08-2011: Version 0.1.1 released

  • Added bsolana run as a composition of all sub-programs
  • Fixed a bug with extraction methylation levels

• 20-07-2011: Version 0.1 released

  • Initial release