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Get documentation ready for release

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Heng Li
2017-07-18 11:04:09 -04:00
parent 71e2a97a4c
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.TH minimap2 1 "12 July 2017" "minimap2-2.0-r174-pre" "Bioinformatics tools"
.TH minimap2 1 "18 July 2017" "minimap2-2.0-r180-dirty" "Bioinformatics tools"
.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences
@@ -326,14 +326,22 @@ cg Z CIGAR string (only in PAF)
.TE
.SH LIMITATIONS
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.TP 2
*
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
hits. If the positions of these minimizer hits are incorrect, the final
alignment may be suboptimal or unnecessarily fragmented.
.TP
*
Minimap2 may produce poor alignments that may need post-filtering. We are still
exploring a reliable and consistent way to report good alignments.
.TP
*
Minimap2 does not work well with Illumina short reads as of now.
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*
Minimap2 requires SSE2 instructions to compile. It is possible to add
non-SSE2 support, but it would minimap2 times slower.
.SH SEE ALSO
.PP
miniasm(1), minimap(1), bwa(1).