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preseq

Version:
2.0.x
Identifier: TL_ec197e.d1
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Sequencing
DNA
Genomics
Prediction and recognition

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Overview

This package is aimed at predicting and number of distinct reads and how many will be expected from additional sequencing using 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.

Associations
Subtools
  • preseq gc_extrap
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  • preseq c_curve

    c_curve computes the expected yield of distinct reads for experiments smaller than the input experiment in a .bed or .bam file through resampling. The full set of parameters can be outputed by simply typing the program name. If output.txt is the desired output file name and input.bed is the input .bed file, then simply type $ preseq c_curve -o output.txt input.sort.bed

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  • preseq lc_extrap

    lc_extrap computes the expected future yield of distinct reads and bounds on the number of total distinct reads in the library and the associated confidence intervals. The -o parameter specifies the output file for the expected future yield. $ preseq lc_extrap -o yield.txt input.sort.bed

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