ngsflows/README.rmd at master · flow-r/ngsflows · GitHub

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### NOTE:
This package has been replaced by [ultraseq](https://github.com/flow-r/ultraseq). All future development and bug fixes will be in towards ultraseq.

ngsflows
----------------------------------------------------

This package host several wrappers for tools. While we have a few example workflows, they are still evolving and may change.


## List of modules


```{bash  }
tree R

```


## Installation:

```r
install.packages('devtools')
library(devtools)
install_github(repo = 'ngsflows', username = 'flow-r')
```


## Downloading resource bundles.

Many of the above tools (like GATK, Mutect) require reference genome files.

These may be downloaded from [Illumina iGenomes](https://support.illumina.com/sequencing/sequencing_software/igenome.html) OR [Broad Insititute](https://www.broadinstitute.org/gatk/guide/article.php?id=1215) OR UCSC.

Due to extensive testing and tool availability its recommended to use the GATK's bundle for Homo Sapiens, for other we can use one from iGenomes.

We have a in built function to get genomes from Illumina (example below).


```
library(ngsflows)
fetch_genomes(species="Homo_sapiens")

################################################
Available Sources:
################################################

Ensembl
NCBI
UCSC

Example:
fetch_genomes species=Homo_sapiens src=NCBI build=build37.2

```