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Originally posted by mido1951
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Oh - I see the confusion. BBMap is not capable of mapping unlimited-length reads. It can only map reads up to 600bp. mapPacBio.sh is a version of BBMap that supports longer reads, up to 6000bp. Reads longer than that will be shredded into shorter pieces which are mapped and tracked individually. So it's not ideal for long read platforms for Nanopore when you need full-length alignments.
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