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r487: demote "map10k"; improved README

This commit is contained in:
Heng Li 2017-10-07 19:19:40 -04:00
parent bf2d4f7aec
commit f150257a0d
3 changed files with 17 additions and 17 deletions
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23
README.md
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@ -10,10 +10,10 @@
git clone https://github.com/lh3/minimap2
cd minimap2 && make
# long reads against a reference genome
./minimap2 -ax map10k test/MT-human.fa test/MT-orang.fa > test.sam
./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam
# create an index first and then map
./minimap2 -x map10k -d MT-human.mmi test/MT-human.fa
./minimap2 -ax map10k MT-human.mmi test/MT-orang.fa > test.sam
./minimap2 -d MT-human.mmi test/MT-human.fa
./minimap2 -a MT-human.mmi test/MT-orang.fa > test.sam
# long-read overlap (no test data)
./minimap2 -x ava-pb your-reads.fa your-reads.fa > overlaps.paf
# spliced alignment (no test data)
@ -108,9 +108,9 @@ regardless of query data types.
Minimap2 uses the same base algorithm for all applications. However, due to the
different data types it supports (e.g. short vs long reads; DNA vs mRNA reads),
minimap2 needs to be tuned for optimal performance and accuracy. You should
usually choose a preset with option **-x**, which sets multiple parameters at
the same time.
minimap2 needs to be tuned for optimal performance and accuracy. It is usually
recommended to choose a preset with option **-x**, which sets multiple
parameters at the same time. The default setting is the same as `map-ont`.
#### <a name="map-long-genomic"></a>Map long noisy genomic reads
@ -161,6 +161,9 @@ be paired if they are adjacent in the input stream and have the same name (with
the `/[0-9]` suffix trimmed if present). Single- and paired-end reads can be
mixed.
Minimap2 does not work well with short spliced reads. There are many capable
RNA-seq mappers for short reads.
#### <a name="full-genome"></a>Full genome/assembly alignment
```sh
@ -226,12 +229,13 @@ It provides C APIs to build/load index and to align sequences against the
index. File [example.c](example.c) demonstrates typical uses of C APIs. Header
file [minimap.h](minimap.h) gives more detailed API documentation. Minimap2
aims to keep APIs in this header stable. File [mmpriv.h](mmpriv.h) contains
additional private unstable APIs which may be subjected to changes frequently.
additional private APIs which may be subjected to changes frequently.
This repository also provides Python bindings to a subset of C APIs. File
[python/README.rst](python/README.rst) gives the full documentation;
[python/minimap2.py](python/minimap2.py) shows an example. This Python
extension, mappy, is also [available from PyPI][mappy] via `pip install`.
extension, mappy, is also [available from PyPI][mappypypi] via `pip install
mappy` or [from BioConda][mappyconda] via `conda install -c bioconda mappy`.
## <a name="limit"></a>Limitations
@ -257,4 +261,5 @@ warmly welcomed.
[ksw2]: https://github.com/lh3/ksw2
[preprint]: https://arxiv.org/abs/1708.01492
[release]: https://github.com/lh3/minimap2/releases
[mappy]: https://pypi.python.org/pypi/mappy
[mappypypi]: https://pypi.python.org/pypi/mappy
[mappyconda]: https://anaconda.org/bioconda/mappy

6
main.c
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@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.2-r486-dirty"
#define MM_VERSION "2.2-r487-dirty"
#ifdef __linux__
#include <sys/resource.h>
@ -231,8 +231,8 @@ int main(int argc, char *argv[])
fprintf(fp_help, " --version show version number\n");
fprintf(fp_help, " Preset:\n");
fprintf(fp_help, " -x STR preset (always applied before other options) []\n");
fprintf(fp_help, " map10k/map-pb: -Hk19 (PacBio/ONT vs reference mapping)\n");
fprintf(fp_help, " map-ont: -k15 (slightly more sensitive than 'map10k' for ONT vs reference)\n");
fprintf(fp_help, " map-pb: -Hk19 (PacBio vs reference mapping)\n");
fprintf(fp_help, " map-ont: -k15 (Oxford Nanopore vs reference mapping)\n");
fprintf(fp_help, " asm5: -k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 (asm to ref mapping; break at 5%% div.)\n");
fprintf(fp_help, " asm10: -k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 (asm to ref mapping; break at 10%% div.)\n");
fprintf(fp_help, " ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n");

5
minimap2.1
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@ -288,11 +288,6 @@ are:
PacBio/Oxford Nanopore read to reference mapping
.RB ( -Hk19 )
.TP
.B map10k
The same as
.B map-pb
.RB ( -Hk19 )
.TP
.B map-ont
Slightly more sensitive for Oxford Nanopore to reference mapping
.RB ( -k15 ).