In flow-r/ngsflows: Robust Pipelines for Next-Generation Sequencing Analysis; A Companion Package for flowr

NOTE:

This package has been replaced by ultraseq.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

tree R

Installation:

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 OR Broad Insititute 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")

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Available Sources:
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Ensembl
NCBI
UCSC

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

flow-r/ngsflows documentation built on May 16, 2019, 1:25 p.m.