Seal: SEquence ALignment evaluation suite
By Jit 2303 days ago
http://compbio.case.edu/seal/
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
