How Do I Assess The Quality Of The Output From My Aligner?

Question

[KCC]

I want to use bwa, novoalign and stampy+bwa on my data and compare the results. What measures should I use to assess the quality of their output and what software if any should I use to do it?

Answer 1

[Istvan Albert]

See the paper A survey of sequence alignment algorithms for next-generation sequencing and a more recent one Comparative analysis of algorithms for next-generation sequencing read alignment

[brentp]

+1 specifically the ROC style curves

Answer 2

[Larry_Parnell]

I would suggest using the metrics discussed in the papers where those aligners are initially described.

Answer 3

[Doctoroots]

Since the tools you mention output the alignment results in SAM format, you can also use SAMStat which outputs some basic alignment stats (mapping / quality / nucleotide composition / etc.) when given a SAM/BAM file.