Seal: SEquence ALignment evaluation suite

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

News

2011-09-08

• Seal 2.1 is released, which adds a command-line option to specify which tools are run.

2011-09-07

• Seal is now hosted on GitHub at http://github.com/mruffalo/seal/.
• Fixed a bug that would occasionally cause a NegativeArraySizeException when generating small indels.

Source Code

• Latest version (packaged as .zip)
• Latest version (packaged as .tar.gz)
• Latest version (packaged as .tar.xz)
• SHA256 digests

A README.txt (containing usage instructions) is included in the archive.

The full version history is available through the Git version control system:

git clone git://github.com/mruffalo/seal.git

Tags in this repository are signed with Matthew Ruffalo's GPG key (fingerprint FF01 0726 CBC6 6DBD E521 5B85 222C 6D4B 11EA AB0E).

Other Downloads

Human Genome, 2 parts

• hg19-1_2.fa (xz compressed version)
• hg19-2_2.fa (xz compressed version)

Acknowledgments

This work was supported in part by National Science Foundation Award IIS-0916102.

I would like to thank the authors of the Apache log4j logging framework and the JCommander command-line argument parsing library.