When it comes to next gen sequencing, here are the top 8 online calculators that we have found:

Coverage

1. Genohub’s shop by project feature
2. The Coverage Calculator by Clinical Genomics

Oligonucleotide

1. The Oligo Calc: Oligonucleotide Properties Calculator by Northwestern University
2. The OligoAnalyzer 3.1 by Integrated DNA Technologies

Primers

1. NCBI/ Primer-BLAST: Finding primers specific to your PCR template (using Primer3 and BLAST) 
2. Primer3: WWW primer tool by UmassMed

qPCR Efficiency

1. The qPCR efficiency calculator by Thermo Scientific
2. The QPCR Standard Curve Slope to Efficiency Calculator by Agilent Technologies

If you know of any other great online calculators for next gen sequencing please tell us about it!