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SMRTSCAPE PacBio coverage estimator

SMRTSCAPE 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 processed subreads, and therefore using the full (raw "polymerase reads") smrtreads=X value for SMRT cells will overestimate coverage.

PacBio coverage options:

Average subread length (bp):

Error-rate per base (bp):

Average 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):

Advanced Options

Target 100% X Coverage for pre-assembly:

Minimum X coverage for anchor subreads:

Efficiency of mapping anchor subreads onto seed reads for correction :


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

© 2016 RJ Edwards. Contact: richard.edwards@unsw.edu.au.