Hi, I have a question about FLASH parameter.

FLASH has a maximum overlap parameter called -M.

And parameter recommend this value that calculated from the read length, fragment size, fragment length standard deviation.

   -r, --read-len=LEN
   -f, --fragment-len=LEN
   -s, --fragment-len-stddev=LEN
                      Average read length, fragment length, and fragment
                      standard deviation.  These are convenience parameters
                      only, as they are only used for calculating the
                      maximum overlap (--max-overlap) parameter.

                      ***The maximum overlap is calculated as the overlap of
                      average-length reads from an average-size fragment
                      plus 2.5 times the fragment length standard
                      deviation.*** 

                      The default values are -r 100, -f 180,
                      and -s 18, so this works out to a maximum overlap of
                      65 bp.  If --max-overlap is specified, then the
                      specified value overrides the calculated value.

So, I made a python code for calculate read length, average read length, standard deviation read length.

I suddenly found that everything is wrong. Because I can't get fragment size. I just have a forward, reverse fastq file.

          -------------------------------------  <fragment>

          ----------------------->                 <forward read>
                          over_lap
                         <-----------------------  <reverse read>

I confused all about that.

I set the -M parameter(max overlap) Avg(forward read length) + 2.5 * (standard deviation(forward read length).

But I think it is wrong. Because FLASH recommended the value like this.

                     The maximum overlap is calculated as the overlap of
                      average-length reads from an average-size fragment
                      plus 2.5 times the fragment length standard
                      deviation.

I think I should know about fragment size. But I just have forward / reverse fastq file.

what do you think I should do? I really need your advice.