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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
commit 495a78e40a
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29
README.md
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@ -8,7 +8,7 @@ cd minimap2 && make
./minimap2 -x map10k -d MT-human.mmi test/MT-human.fa ./minimap2 -x map10k -d MT-human.mmi test/MT-human.fa
./minimap2 -ax map10k MT-human.mmi test/MT-orang.fa > test.sam ./minimap2 -ax map10k MT-human.mmi test/MT-orang.fa > test.sam
# long-read overlap (no test data) # long-read overlap (no test data)
./minimap2 -x ava10k your-reads.fa your-reads.fa > overlaps.paf ./minimap2 -x ava-pb your-reads.fa your-reads.fa > overlaps.paf
# man page # man page
man ./minimap2.1 man ./minimap2.1
``` ```
@ -21,24 +21,35 @@ reference genome optionally with detailed alignment (i.e. CIGAR). At present,
it works efficiently with query sequences from a few kilobases to ~100 it works efficiently with query sequences from a few kilobases to ~100
megabases in length at an error rate ~15%. Minimap2 outputs in the [PAF][paf] or megabases in length at an error rate ~15%. Minimap2 outputs in the [PAF][paf] or
the [SAM format][sam]. On limited test data sets, minimap2 is over 20 times the [SAM format][sam]. On limited test data sets, minimap2 is over 20 times
faster than most other long-read aligners. faster than most other long-read aligners. It will replace BWA-MEM for long
reads and contig alignment.
Minimap2 is the successor of [minimap][minimap]. It uses a similar Minimap2 is the successor of [minimap][minimap]. It uses a similar
minimizer-based indexing and seeding algorithm, and improves the original minimizer-based indexing and seeding algorithm, and improves the original
minimap with homopolyer-compressed k-mers (see also [SMARTdenovo][smartdenovo] minimap with homopolyer-compressed k-mers (see also [SMARTdenovo][smartdenovo]
and [longISLND][longislnd]), better chaining and the ability to produce CIGAR and [longISLND][longislnd]), better chaining and the ability to produce CIGAR
with fast extension alignment (see also [libgaba][gaba] and [ksw2][ksw2]) and with fast extension alignment (see also [libgaba][gaba] and [ksw2][ksw2]) and
two-piece affine gap cost. piece-wise affine gap cost.
## Limitations ## Limitations
At the alignment phase, minimap2 performs global alignments between minimizer * At the alignment phase, minimap2 performs global alignments between minimizer
hits. If the positions of these minimizer hits are incorrect, the final alignment hits. If the positions of these minimizer hits are incorrect, the final
may be suboptimal or broken due to the Z-drop heuristics. In addition, in the alignment may be suboptimal or unnecessarily fragmented.
event of a long insertion/deletion, minimap2 may split the long event into
a few smaller events. We will address these issues in future. * Minimap2 may produce poor alignments that may need post-filtering. We are
still exploring a reliable and consistent way to report good alignments.
* Minimap2 does not work well with Illumina short reads as of now.
* Minimap2 requires SSE2 instructions to compile. It is possible to add
non-SSE2 support, but it would minimap2 times slower.
In general, minimap2 is a young project with most code written since June,
2017. It may have bugs and room for improvements. Bug reports and suggestions
are warmly welcomed.
Minimap2 does not work well with Illumina short reads as of now.
[paf]: https://github.com/lh3/miniasm/blob/master/PAF.md [paf]: https://github.com/lh3/miniasm/blob/master/PAF.md
[sam]: https://samtools.github.io/hts-specs/SAMv1.pdf [sam]: https://samtools.github.io/hts-specs/SAMv1.pdf

2
main.c
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@ -10,7 +10,7 @@
#include "minimap.h" #include "minimap.h"
#include "mmpriv.h" #include "mmpriv.h"
#define MM_VERSION "2.0-r180-pre" #define MM_VERSION "2.0-r180-dirty"
void liftrlimit() void liftrlimit()
{ {

22
minimap2.1
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@ -1,4 +1,4 @@
.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 .SH NAME
.PP .PP
minimap2 - mapping and alignment between collections of DNA sequences minimap2 - mapping and alignment between collections of DNA sequences
@ -326,14 +326,22 @@ cg Z CIGAR string (only in PAF)
.TE .TE
.SH LIMITATIONS .SH LIMITATIONS
.PP .TP 2
*
At the alignment phase, minimap2 performs global alignments between minimizer At the alignment phase, minimap2 performs global alignments between minimizer
hits. If the positions of these minimizer hits are incorrect, the final alignment hits. If the positions of these minimizer hits are incorrect, the final
may be suboptimal or broken due to the Z-drop heuristics. In addition, in the alignment may be suboptimal or unnecessarily fragmented.
event of a long insertion/deletion, minimap2 may split the long event into .TP
a few smaller events. We will address these issues in future. *
.PP 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. Minimap2 does not work well with Illumina short reads as of now.
.TP
*
Minimap2 requires SSE2 instructions to compile. It is possible to add
non-SSE2 support, but it would minimap2 times slower.
.SH SEE ALSO .SH SEE ALSO
.PP .PP
miniasm(1), minimap(1), bwa(1). miniasm(1), minimap(1), bwa(1).