SOLiD™ System Color Space Mapping Tool (mapreads)

Description

• The SOLiD™ System Color Space Mapping Tool (mapreads) is a mapping tool for SOLiD™ system sequencing reads. The input for the tool is a reference genome in fasta format and a SOLiD™ system read file in .csfasta format.  The package will find all the hits (up to first Z hits with the user specified Z-parameter) for each read and the reference sequence allowing up to N mismatches. The mapping is performed in color space with the translation of the reference sequence done on-the-fly.  The user has the option of counting valid adjacent mismatches as either 1 or 2. The package also allows  the user to utilize quality values in the mapping procedure and also supports the use of IUB code to represent known SNPs in the genome.
  

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 Bioysystems

Documenation

• User manual for this package

Software Download

• This software is distributed as source code.  The current version of the SOLiD™ System Analysis Pipeline Tool (mapreads) can be downloaded here.
• The schemas associated with the package can be downloaded here.

Sample Data Download

• E. Coli sample data for this software tool can be downloaded here.
• Human sample data for this software tool can be downloaded here.