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?