gt-simreads(1) Simulate sequencing reads from random positions in the input sequence(s).


gt simreads [option ...] <encseq>


-num [value]

desired number of reads (default: undefined)

-coverage [value]

desired coverage of the reads (default: undefined)

-len [value]

fixed read length (default: undefined)

-minlen [value]

minimal read length (default: undefined)

-maxlen [value]

maximal read length (default: undefined)

-distlen [string]

use read length distribution file (in the output format of the seqstat tool) (default: undefined)

-o [filename]

redirect output to specified file (default: undefined)

-gzip [yes|no]

write gzip compressed output file (default: no)

-bzip2 [yes|no]

write bzip2 compressed output file (default: no)

-force [yes|no]

force writing to output file (default: no)

-p [yes|no]

show a progress bar (default: no)

-v [yes|no]

be verbose (default: no)

-ds [string]

output distribution of starting positions to specified file (default: undefined)

-dl [string]

output distribution of read lengths to specified file (default: undefined)

-ss [yes|no]

simulate reads in forward direction only (default: no)


display help for basic options and exit


display help for all options and exit


display version information and exit


Report bugs to <[email protected]>.