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preseq lc_extrap

By Daley T., Smith A.D., Last update 1494699000
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lc_extrap description

lc_extrap uses rational function approximations of Good and Toulmins non-parametric empirical Bayes estimator to predict the yield of future experiments, in essence looking into the future for hypothetical experiments. It is used to predict the yield and then c curve can be used to check the yield from the larger experiment. Output is a text file with four columns. The first is the total number of reads, second gives the corresponding average expected number of distinct reads, and the third and fourth give the lower and upper limits of the confidence interval. Specifying verbose will print out the counts histogram of the input file

Parent program: Preseq

The preseq package is aimed at predicting the yield of distinct reads from a genomic library from an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples