Hello everybody,
I just started working with mate-pair data from Illumina and I am a bit lost regarding which aligners can actually work with mate-pairs. Most aligners work with paired-ends but I am starting to realize that that does not mean they work with mate-pairs as well.
Am I correct that bwa can only work with paired-end reads but not mate-pairs?
How about Novoalign? I could not find an explicit mention to mate-pairs but I could easily have overlooked it.
Mosaik does work with mate-pairs but MosaikSort won't work if more than 10% of the reads have paired-end orientation (which unfortunately happens in some samples due to contamination).
I would be very grateful if people could share their experience working with mate-pairs.
Thanks!!
I just started working with mate-pair data from Illumina and I am a bit lost regarding which aligners can actually work with mate-pairs. Most aligners work with paired-ends but I am starting to realize that that does not mean they work with mate-pairs as well.
Am I correct that bwa can only work with paired-end reads but not mate-pairs?
How about Novoalign? I could not find an explicit mention to mate-pairs but I could easily have overlooked it.
Mosaik does work with mate-pairs but MosaikSort won't work if more than 10% of the reads have paired-end orientation (which unfortunately happens in some samples due to contamination).
I would be very grateful if people could share their experience working with mate-pairs.
Thanks!!
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