What are the best ways and tools for analysis in supply chain?

Best way to Analyse Supply Chain is

First Sales Forecast should be accurate.

Sales Forecast can be calculted by the historical trend.

Sales Planning and Demand Forecasting is also important.

Based on above prepare a sales plan

Capacity calculation of Production Line, Warehouse Capacity, should be calculated

Production Planning and Execution 

Purchase Planning, 

Inventory Management

etc

using value chain maping

Analyze the sequence with the approach of water theory

Budgeting process will help alot in this analysis