How to use Novoalign Paired End mode in command line?

[dpryan]

Well, it's not really that different for simple cases:

novoalign -d index -o SAM -f read1 read2

I guess you don't really need "-o SAM", but the output won't be as useful otherwise.

Edit: I should mention that "index" is just a placeholder for whatever you called the index/database/whatever-novoindex-calls-it and read1/read2 are the fastq files for reads 1 and 2, respectively.

[prs321]

Ya, but the syntax is too confusing. I'm simply just trying to take my pair-end reads and align them to the reference genome.

I have mastered it in BWA already, but I was told to try novoalign. In BWA, I only had to enter in 3 options essentially, pair1, pair2, and the ref.

[dpryan]

Did you go through the quick start tutorial? The examples there are short.

[prs321]

Topic.

The documentation appears to be too confusing. All I need to know is how to enter my input in the command line so I can get the output.