NAME

       dsimulator - generate synthetic reads for a random genome

SYNOPSIS

       dsimulator    genlen:double    [-cdouble(20.)]   [-bdouble(.5)]   [-rint]   [-mint(10000)]
       [-sint(2000)][-xint(4000)] [-edouble(.15)][-Mfile]

DESCRIPTION

       dsimulator first generates a fake genome of size genlen*1Mb long, that has an  AT-bias  of
       -b.   It  then  generates  sample  reads  of  mean  length  -m  from  a  log-normal length
       distribution with standard deviation -s, but ignores reads of length  less  than  -x.   It
       collects  enough reads to cover the genome -c times and introduces -e fraction errors into
       each read where the ratio of insertions, deletions, and substitutions are set  by  defined
       constants  INS_RATE  (default  73%) and DEL_RATE (default 20%) within generate.c.  One can
       also control the rate at which reads are picked from the forward and  reverse  strands  by
       setting  the  defined  constant FLIP_RATE (default 50/50).  The -r option seeds the random
       number generator for the generation of the genome so that one  can  reproducibly  generate
       the  same underlying genome to sample from.  If this parameter is missing, then the job id
       of the invocation seeds the random number generator.  The output is sent to  the  standard
       output (i.e.  it is a UNIX pipe).  The output is in Pacbio .fasta format suitable as input
       to fasta2DB(1).  Finally, the -M option requests that the coordinates from which each read
       has  been  sampled  are  written  to the indicated file, one line per read, ASCII encoded.
       This "map" file essentially tells one where every read belongs in an assembly and is  very
       useful  for  debugging  and testing purposes.  If a read pair is say b,e then if b < e the
       read was sampled from [b,e] in the forward direction, and  if  b > e  from  [e,b]  in  the
       reverse direction.

SEE ALSO

       daligner(1)