loresim2

Long read simulation.

Source

The loresim source code is hosted on github:

git@github.com:gt1/loresim.git

Compilation of loresim

loresim needs libmaus2 [https://github.com/gt1/libmaus2] . When libmaus2 is installed in ${LIBMAUSPREFIX} then biobambam2 can be compiled and installed in ${HOME}/biobambam2 using

- autoreconf -i -f
- ./configure --with-libmaus2=${LIBMAUSPREFIX} \
	--prefix=${HOME}/biobambam2
- make install

Contained programs

fastareformat: reformats FastA or FastQ so it becomes valid input for the DAZZ_DB tool fasta2DB. This includes changing read names and wrapping long lines.

longreadsim: generates a sequence of random DNA reads from a given sequence. For this the input sequence is traversed a number of times and split into pieces which are subsequently either modified within a certain error range or dropped with a certain rate. The program can switch between a low and high error profile during read generation. Reads are randomly taken from the forward or reverse strand. The program has the following options

• readlenavg: average read length (default: 15k)
• readlenstddev: standard deviation for read length (default: 3k)
• droprate: probability for dropping a read (default: 0.01)
• numtraversals: number of traversals of the input sequence (default: 1)
• startlowprob: probability of starting a read in low error mode (default: 0.7)
• keeplowstate: probability of staying in low error mode when in low error mode (default: 0.9998)
• keephighstate: probability of staying in high error mode when in high error mode (default: 0.995)
• eratelow: low error mode error rate average
• eratelowstddev: standard deviation of error rate in low error mode
• eratehigh: high error mode error rate average
• eratehighstddev: standard deviation of error rate in high error mode
• placerandom: randomly place reads instead of performing linear traversal (default 0). This produces output data with uneven coverage following a Poisson distribution.