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