How to proceed after contigs.fa file obtained from VELVET assembly I want to assemble a linear genome and I have a reference genome too.

I ran the following commands for de novo velvet assembly: 

velveth auto 31,45,2 -fastq -shortPaired1 -separate 2-CA-SVA-2_S2_L001_R1_001.fastq 2-CA-SVA-2_S2_L001_R2_001.fastq


I chose auto_33 for further analysis

velvetg auto_33 -exp_cov auto


Now my output files inside auto_33 folder are:

contigs.fa
Graph2
LastGraph
Log
PreGraph
Roadmaps
Sequences
stats.txt


But I have no clue how to move ahead. Can I do anything else with velvet or do I have to switch to another program?
The contigs.fa file is a FASTA formatted file of the final contigs generated by velvet.  I would start assessing the quality of the assembly that was generated. Here are some questions to get you started.  Really the next steps depend on how you plan to use the assembly.

What is the distribution of contig lengths? Average and N50 contig length

How does the assembly compare to the reference?


How much of the reference does the assembly cover?


When you align the original reads back to the contigs how well are they covered? 


Do any of the read alignments not make sense? 
Are there sections of the contigs that are not covered?