Hi,
I'm trying to compare sequences from several different libraries sequenced at different times. Consequently they differ in read length from about 35bp to 150bp. I'm planning on using BWA but I'm sure whether I should use BWA mem or BWA backtrack. BWA mem seems superior for reads 70bp+ but some of my samples are shorter than that. I'd also like to use the same aligner for all my samples for consistency sake.
So the question is how does BWA mem do on short read samples? The manual says it is not recommended, but how much worse is it? Is there another good option for aligning libraries with such different read sizes?
Thanks
I'm trying to compare sequences from several different libraries sequenced at different times. Consequently they differ in read length from about 35bp to 150bp. I'm planning on using BWA but I'm sure whether I should use BWA mem or BWA backtrack. BWA mem seems superior for reads 70bp+ but some of my samples are shorter than that. I'd also like to use the same aligner for all my samples for consistency sake.
So the question is how does BWA mem do on short read samples? The manual says it is not recommended, but how much worse is it? Is there another good option for aligning libraries with such different read sizes?
Thanks
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