SOLiD™ BaseQV Tool (gffToSam)

Description

• This software takes SOLID^TM3  output files as input and converts them to a format which contains base sequence and quality values associated with these base sequences (SAM). It supports both mates and fragment-sorted output files. Using color space rules, it uses color quality values to predict base quality values, given the annotations generated by the base translation algorithm in the GFF file. Other features include generation of mate flags in SAM format, generation of MD and CIGAR tags, and ASCII-space quality values. For GFF mate-pair files sorted by position, automated split-and-merge of reads into chromosomes guarantees minimal memory usage. This also guarantees correct flags for each mate pair. The program supports parameters for SAM header settings and generates a Read Group (RG) tag for each of the reads. The color space reads and color quality values are all in 5’ to 3’ orientation; in contrast, the base reads and base quality values are represented on the forward genomic strand.

Licensing

• This software is being licensed to you under the OSI compliant GNU Public License (GPL). Please read the license in its entirety and ensure that you understand the licensing conditions for use. Your use of this software indicates your acceptance of this licensing agreement. Click on this link to read the licensing agreement.

Support

• This tool is being released as "unsupported software" by Applied Biosystems.

Packages

Pre-Bioscope™ Tool

• The current version of the tool can be downloaded here.
• Documentation and Release notes for this software can be found here.
• A sample dataset can be downloaded here.

Source Distribution (please note that this is a source ONLY distribution of a Bioscope algorithm and available through SVN checkout)

• Please contact website support to recieve access information
• The current version of the source can be downloaded here.
• Documentation and Release notes for this software can be found here.
• A sample dataset can be downloaded here.