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PacBio coverage estimator

This module estimates the % genome coverage and accuracy for different X coverage of a genome using PacBio sequencing, i.e. assuming a non-biased error distribution. Calculations use binomial/poisson distributions, assuming independence of sites. Accuracy is based on >50% reads covering a particular base having the correct call. Assuming random calls at the other positions, 25% of the “wrong” positions will be correct by chance. In reality, it will be even higher than this, assuming majority calls are used. Wrong calls will be split between three possible incorrect bases. Accuracy is therefore a conservative estimate.

All calculations are based on assembled reads, and therefore using the full smrtreads=X value for SMRT cells will overestimate coverage.

PacBio coverage options:

Average assembled read length (bp):

Error-rate per base (bp):

Average assembled output per SMRT cell:

Genome size (bp):

Maximmum X coverage to calculate:

Output estimated coverage by SMRT cell rather than X coverage:

List of %X coverage values to report (comma separated):

Run

After running, click on the coverage tab to see results for different X Coverage and SMRT cells numbers.


© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.