BOL

Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including:

• Reading a pre-existing reference genome from one or more FASTA files.
• Alternatively, generating an artificial reference genome based on input parameters (length, repeat count, repeat length, repeat variability rate).
• Simulating reads from random locations in the genome based on input parameters of read length, coverage, sequencing error rate, and indel rate.
• Applying alignment tools to the genome and the reads through a standardized interface.
• Parsing the output of the alignment tool and calculating the number of reads that were correctly or incorrectly mapped.
• Computing run times and measures of accuracy.

Seal has interfaces to evaluate the following software packages:

• Bowtie
• BWA
• MAQ
• mrFAST
• mrsFAST
• Novoalign
• SHRiMP
• SOAPv2