Experiments to understand how assemblers handle repeat regions.
Examples:
sim.pl data/AB-AIB.fa
Simulate reads from the AB-AIB FASTA file and assemble them with velvet and SPAdes.
sim.pl -e 0 -c 30 -a data/ABC-AIBIC.fa
Simulate error free reads at 30X coverage and plot all-to-all matches in the 'reference vs assembly' dot plot.
Usage: sim.pl [options] ref.fa
-h - print this help statement
-a - show all to all matches in reference vs assembly dot plot
-c cov - fold coverage used in simulating reads (D: 20)
-e fract - fraction of standard Illumina HiSeq 2000 error rate (D: 1.0)
-l len - simulated read length (D: 100)
-m mean - mean of paired end read fragment size (D: 300)
-s stdev - standard deviation of read fragment size (D: 10)