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added limitations

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Heng Li 2017-07-01 12:11:56 -04:00
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minimap2.1
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@ -275,6 +275,15 @@ nn i Number of ambiguous bases in the alignment
cg Z CIGAR string (only in PAF)
.TE
.SH LIMITATIONS
.PP
At the alignment phase, minimap2 performs global alignments between minimizer
hits. If the positions of these minimizer hits are incorrect, the final alignment
may be suboptimal or broken due to the Z-drop heuristics. In addition, in the
event of a long insertion/deletion, minimap2 may split the long event into
a few smaller events. We will address these issues in future.
.PP
Minimap2 does not work well with Illumina short reads as of now.
.SH SEE ALSO
.PP
miniasm(1), minimap(1), bwa(1).