WATSTATS(1)      OGMP SEQUENCING PROJECT MANAGEMENT UTILITY     WATSTATS(1)

NAME
    watstats - Calculate and print tables of statistics and expected
               values related to a shotgun sequencing project.

DESCRIPTION
    watstats is a program that asks for four parameters related to
    a shotgun sequencing project:

            G = The genome size in kbp,
            N = The number of readings,
            L = The average length of those readings in bp,
        and T = The minimum number of bp needed to recognise sequence overlaps,

    and calculates the following values, functions of those parameters:

            c = The redundancy of coverage,
        E(Nc) = The expected number of contigs,
        E(Sc) = The expected number of readings per contig,
        E(Lc) = The expected length of each contig,
     and   %c = The percentage of coverage of the genome.

    Of the four parameters interactively asked for (G, N, L or T), at most
    one of them can be a "range specification". Such a specification is
    a list of three integer numbers separated by anything else, like
    this: "200-500,100" or "From 200 to 500 by steps of 100" or
    "xyz200beatles500&!%100". Such a specification is interpreted like
    in the second example just mentionned: the first number is a START
    value, the second number a END value and the third one a STEPping
    value. When a range specification is given to G, N, L or T parameter,
    then watstats will print a table of the c, E(Nc), E(Sc), E(Lc)
    and %c values with that parameter changing from START to END by
    increments of STEP.
   
OPTION
    -O This is the "ocean option". When present, watstat will ask for
    one more parameter besides G, N, L and T. This parameter is

            O = A threshold ocean size in bp.

    An ocean is a gap between two contigs, after assembly. The O parameter
    will be used to compute a supplementary value:

           %o = The probability of having an ocean > O bp after assembly.

FORMULAS

    All these formulas are from [Lander, Waterman], except for the %c
calculation which is a simple equation figured out by PR. Let

           GM = G*1000 (The genome size in bp),
        theta = T/L,
        sigma = 1-theta.

    Then

            c = L*N/GM,
        E(Nc) = N*exp(-c*sigma),
        E(Sc) = exp(c*sigma),
        E(Lc) = L*[((exp(c*sigma)-1)/c)+(1-sigma)],
           %c = E(Nc)*E(Sc)/G (converted to percentage),
           %o = exp(-c*(O/L+theta)).

REFERENCE
    Lander, E. S. and Waterman, M. S., "Genomic mapping by fingerprinting
    random clones: a mathematical analysis", Genomics 2, 231-239 (1988).

AUTHOR
    Pierre Rioux,
    Tim Littlejohn (Project Management),
    Organelle Genome Megasequencing Project, Oct. 1994.
    Also see the REFERENCE section.