xenial (1) dsimulator.1.gz

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)