SEAL Sequencing Simulation/Evaluation Suite 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 == Prerequisites == * Some type of Linux distribution. Cygwin may work but has not been tested. * Java 1.6. Sun Java is preferred; OpenJDK should work but has not been tested. * Each alignment tool that you'd like to evaluate must be in your PATH. * At least 8GB RAM depending on your usage (large numbers of reads and larger genomes may require more). == Usage Instructions == 1. Enter the 'build' directory, and append the required .jar files to your CLASSPATH environment variable: $ . classpath.sh 2. Run the appropriate evaluation program (one of the following:) $ java -Xmx16G ErrorRateEvaluation $ java -Xmx16G GenomeSizeEvaluation $ java -Xmx16G IndelFrequencyEvaluation $ java -Xmx16G IndelSizeEvaluation $ java -Xmx16G ReadCountEvaluation == Notes == The "16G" memory usage is a suggestion that's based on the default genome sizes and read counts; with a 500Mbp generated genome and 100,000 reads you may need as little as 4GB. This memory usage is for SEAL itself, not each alignment tool that is evaluated. Each evaluation program accepts command-line options to specify which genome to use, parameter values, etc. To view the options for each program, run e.g. $ java ErrorRateEvaluation --help Parameter values must be specified as a comma-separated list with no spaces between elements, e.g. $ java -Xmx16G ErrorRateEvaluation --error-rates 0.0,0.1,0.2 Defined genomes for accuracy simulations: * HUMAN_CHR22 * HUMAN * RANDOM_EASY * RANDOM_HARD RANDOM_EASY and RANDOM_HARD specify randomly generated genomes; "easy" signifies no repeats, "hard" specifies 100 repeats of length 500bp each. If you specify HUMAN_CHR22, this data (in FASTA format) will be read from the file "build/data/chr22.fa". HUMAN requires *two* FASTA files: "build/data/hg19-1_2.fa" and "build/data/hg19-2_2.fa". These files can be obtained from the SEAL website, or can be produced by concatenating chromosome FASTA files together. (The human genome is split into two pieces of length ~1.5Gbp to avoid a limitation in Java: Strings cannot have length greater than Integer.MAX_VALUE = 2^31 - 1). Results are written in CSV format to "build/data/[eval_type]_[genome].csv". The accuracy format is: Tool,ErrorRate,Threshold,Precision,Recall,Time,UsedReadRatio The runtime format is: Tool,GenomeSize,ReadCount,PreprocessingTime,AlignmentTime,PostprocessingTime, TotalTime