The best choice is to use the software that is installed on the instrument. If you take an other software you will have to convert your data (when possible). Most of the time you are authorized to install this software on several computer for free. 

On other opportunity, you should try MassHunter Quantitative/Qualitative Analysis. As I know, you can calculate S/N ratio, peaks height and areas of course but you can use also calibration curve and/or correction for RT.

An other software is Metabolite Detector. This one is freely available and very nice. You don't need to spend so much time to learn how to use it, but you cannot controlled everything as in MassHunter.

http://md.tu-bs.de/node/10

(Better to use under Linux). 

If you want to use one of these software, as Laurent mentioned, you have to convert your raw data. 

yes Lemee sir is right.. better you go for the installed software on the instrument..

Clarity Offline from @DataApex allows allows users to evaluate data and prepare methods. Supported import/export file formats include *.CDF, *.MZDATA, *.MZXML and *.MZML, AIA, EZChrom, text files. Users can work with acquired data on computers located anywhere. It provides all the standard functions of Clarity Software except data acquisition and controlling instruments (control modules are accessible for method preparation). The software works with the same files and provides the same outputs (printing and exporting) as the Clarity station. Free demo available for download.

For the RT correction, peak heights etc. GC-LC Concordance solves automatically the retention time shifts between two chromatograms or many (QC, Norm, R&D etc.) + other applications in RI like the automatic identification of all molecules (like in MS) in a chromatogram (FID or MS etc.) in one second.

For more details: http://www.chromatography-gc.com/

i disagree with the two comments that the “best is the instrument vendor solution” as that was neither the question nor is it always accurate. more than a few vendor solutions are terrible and people are si,ply used to crappy analysis of what might actually be good data

@ William Thomas Hiscock can you share these software with me Chromeleon 7.2 Chromatography Data System and TraceFinder 3.2 Software

You can try OpenChrom[1].

It's free of charge, open source and enterprise support possible if you really need it.

[1] https://github.com/OpenChrom/openchrom

Alexander Kerner Dear thanks for sharing.i have tried to chemstation but NIST library was not working with it..so whats should do

Hi Dr- Hafiz Muhammad Rizwan , maybe this helps:

https://github.com/OpenChrom/openchrom/wiki/Peak-Identification-NIST

Alexander Kerner Thanks , I WILL TRY THIS

try this http://models.life.ku.dk/paradise

Try WsearchPro

clarity offline chromatography station

Ashraf M. Sherif thank you very much

Mar Vilanova thanks,

Bekzod Bahromovich Khakimov thanks