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biopet.biopet
Commits
b0289eef
Commit
b0289eef
authored
Jul 28, 2015
by
Peter van 't Hof
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Fixed link
parent
761cb9f5
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docs/pipelines/basty.md
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b0289eef
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@@ -7,7 +7,7 @@ Basty is a pipeline for aligning bacterial genomes and detecting structural vari
Basty will output phylogenetic trees, which makes it very easy to look at the variations between certain species or strains.
### Tools for this pipeline
*
[
Shiva
](
../pipelines/
shiva.md
)
*
[
Shiva
](
shiva.md
)
*
[
BastyGenerateFasta
](
../tools/BastyGenerateFasta.md
)
*
<a
href=
"http://sco.h-its.org/exelixis/software.html"
target=
"_blank"
>
RAxml
</a>
*
<a
href=
"https://github.com/sanger-pathogens/Gubbins"
target=
"_blank"
>
Gubbins
</a>
...
...
@@ -25,7 +25,7 @@ Each aligner has his own way of creating index files. Therefore the options for
### Configuration
To run Basty, please create the proper
[
Config
](
../general/config.md
)
files.
Batsy uses the
[
Shiva
](
../
shiva.md
)
pipeline internally. Please check the documentation for this pipeline for the options.
Batsy uses the
[
Shiva
](
shiva.md
)
pipeline internally. Please check the documentation for this pipeline for the options.
#### Required configuration values
...
...
docs/pipelines/shiva.md
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b0289eef
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@@ -121,7 +121,7 @@ To view all possible config options please navigate to our Gitlab wiki page
| vcffilter | filter_ref_calls | Boolean | true | Remove reference calls |
| vcfstats | reference | String | Path to reference to be used by
`vcfstats`
|
Since Shiva uses the
[
Mapping
](
../
mapping.md
)
pipeline internally, mapping config values can be specified as well.
Since Shiva uses the
[
Mapping
](
mapping.md
)
pipeline internally, mapping config values can be specified as well.
For all the options, please see the corresponding documentation for the mapping pipeline.
### Modes
...
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