Basic usage

nikto -h example.com

There isnt much output, so you generally dont know whats happening, so it might be good to enable verbose output:

nikto -Display V -h example.com

One of the great things you can do with nikto is to specify the type of checks it runs:
from the man page:

  -Tuning
           Tuning options will control the test that Nikto will use against a
           target. By default, if any options are specified, only those tests
           will be performed. If the "x" option is used, it will reverse the
           logic and exclude only those tests. Use the reference number or
           letter to specify the type, multiple may be used:

           0 - File Upload

           1 - Interesting File / Seen in logs

           2 - Misconfiguration / Default File

           3 - Information Disclosure

           4 - Injection (XSS/Script/HTML)

           5 - Remote File Retrieval - Inside Web Root

           6 - Denial of Service

           7 - Remote File Retrieval - Server Wide

           8 - Command Execution / Remote Shell

           9 - SQL Injection

           a - Authentication Bypass

           b - Software Identification

           c - Remote Source Inclusion

           x - Reverse Tuning Options (i.e., include all except specified)

           The given string will be parsed from left to right, any x characters
           will apply to all characters to the right of the character.

Specifying the test

So, to only perform an SQL injection test against your target:

nikto -Tuning 9 -h example.com

or to do everything except DOS

nikto -Tuning x 6 -h example.com

Saving results

You can output to a file with the -o option
You can specify the format of the output file with -Format [csv htm txt or xml]

eg to perform an SQL injection test and save results to an html file with verbose output for your terminal:

nikto -Display V -o results.html -Format htm -Tuning 9 -h example.com
NIKTO

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