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Estimating coverage in metagenomes

Nonpareil uses the redundancy of the reads in a metagenomic dataset to estimate the average coverage and predict the ammount of sequences that will be required to achieve "nearly complete coverage", defined as ≥95% or ≥99% average coverage.

You can use Nonpareil on-line (see an example) or stand-alone. If you use Nonpareil, please cite:

Reference for Nonpareil
Rodriguez-R LM & Konstantinidis KT (2014). Nonpareil: A redundancy-based approach to assess the level of coverage in metagenomic datasets. Bioinformatics 30 (5): 629-635.
On the importance of coverage estimations
Rodriguez-R LM & Konstantinidis KT (2014). Estimating coverage in metagenomic data sets and why it matters. ISME J 8: 2349-2351.