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minor doc improvements

This commit is contained in:
Heng Li 2018-02-12 22:27:02 -05:00
parent 874b8c4795
commit 3b17d62ccd
1 changed files with 26 additions and 7 deletions
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misc/README.md
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@ -40,18 +40,37 @@ Linux or Mac, you can download the precompiled k8 binary with:
curl -L https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2 | tar -jxf -
cp k8-0.2.4/k8-`uname -s` $HOME/bin/k8 # assuming $HOME/bin in your $PATH
```
It is highly recommended to copy the executable `k8` to a directory on your
`$PATH` such as `/usr/bin/env` can find it. Like python scripts, once you
install `k8`, you can launch these k8 scripts either with
install `k8`, you can launch paftools.js in one of the two ways:
```sh
path/to/paftools.js
path/to/paftools.js # only if k8 is on your $PATH
k8 path/to/paftools.js
```
or with
In a nutshell, paftools.js has the following commands:
```sh
k8 path/to/paftools.js
```
Usage: paftools.js <command> [arguments]
Commands:
view convert PAF to BLAST-like (for eyeballing) or MAF
splice2bed convert spliced alignment in PAF/SAM to BED12
sam2paf convert SAM to PAF
delta2paf convert MUMmer's delta to PAF
gff2bed convert GTF/GFF3 to BED12
stat collect basic mapping information in PAF/SAM
liftover simplistic liftOver
call call variants from asm-to-ref alignment with the cs tag
bedcov compute the number of bases covered
mapeval evaluate mapping accuracy using mason2/PBSIM-simulated FASTQ
mason2fq convert mason2-simulated SAM to FASTQ
pbsim2fq convert PBSIM-simulated MAF to FASTQ
junceval evaluate splice junction consistency with known annotations
ov-eval evaluate read overlap sensitivity using read-to-ref mapping
```
paftools.js seamlessly reads both plain text files and gzip'd text files.
@ -104,8 +123,8 @@ default.
### <a name="oveval"></a>Evaluating read overlap sensitivity
Script [ov-eval.js](ov-eval.js) takes sorted read-to-reference alignment and
read overlaps in PAF as input, and evaluates the sensitivity. For example:
Command **ov-eval** takes *sorted* read-to-reference alignment and read
overlaps in PAF as input, and evaluates the sensitivity. For example:
```sh
minimap2 -cx map-pb ref.fa reads.fq.gz | sort -k6,6 -k8,8n > reads-to-ref.paf