100,000 reads (read pairs) are simulated the human genome with wgsim. In this simulation, we first
simulate a diploid genome containing about 28.6 million SNPs and short INDELs
and then simulate error free reads from the diploid genome. Although
reads are error free, many reads cannot be perfectly mapped to the reference
genome due to the presence of variations. The exact wgsim command lines are
(the first for single-end and the second for paired-end):
Evaluated programs and command lines
Default configurations are attempted unless the default certainly fails or the
documentation explicitly suggests better configurations for 100bp HiSeq reads.
Probably the options in use are suboptimal for bowtie-v1 and soap2. The
detailed command lines are:
Paired-end reads are mapped with the following command lines:
The accuracy of each mapper is evaluated by the wgsim_eval.pl script which
regards a mapping is correct if it is within 50bp of the simulated position.
The command line is: