IMPORTANT NOTE: Our servers will undergo a maintenance outage scheduled Thu, Jan 19, 6:00AM (EST). Any jobs that are not completed by that time will be postponed, there is no need to resubmit jobs. You can continue to submit tasks, but they won't be processed until the system is back (see updates). The website will come back to normal operations on Sat, Jan 21, 10:00PM (EST).

Nonpareil

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.