Recommended program for evaluating aligner sensitivity

Question

[fiona.newberry]

I am assessing 6 aligners and need to make roc curves to show the sensitivity and specificity of the aligners.

Can anyone recommend a program that can assess the resulting reads? I was going to use dwgsim_eval but my reads were not simulated with dwgsim. I need to extract false positive and true positive rates for the roc curves

Thanks

Answer 1

[mark.ziemann]

You could try Teaser.

[fiona.newberry]

Thank you. Could I use Teaser if I already generated the simulated reads? I am reading about it and it appears that it can only be used with the reference genome (simulates reads itself).

[mark.ziemann]

I would go with Teaser if I were you. But if you have a specific need outside of the scope of it you could simulate the reads yourself (use ART) then use bedtools/awk to determine whether reads were mapped near the expected position with the expected orientation. This will at least get you some sensitivity/specificity data that you can use in ROC plots.

[fiona.newberry]

Teaser looks good. Apparently I can provide my own simulation. Thanks again