mk_subread_index: Make a Subread index

In wevanjohnson/animalcules.preprocess: This package contains tools and functions for preprocessing microbiome data

Description

This function is a wrapper for the Rsubread::buildindex function. It will generate one or more Subread indexes from a .fasta file. If the library is too large (default >4GB) it will automatically be split into multiple indexes, with _1, _2, etc at the end of the ref_lib basename.

Usage

mk_subread_index(ref_lib, split = 4, mem = 8000)

Arguments

ref_lib	The name/location of the reference library file, in (uncompressed) .fasta format
split	The maximum allowed size of the genome file (in GB). If the ref_lib file is larger than this, the function will spolt the library into multiple parts
mem	The maximum amount of memory (in MB) that can be used by the index generation process (used by the Rsubread::buildindex function)

Value

Returns one or more Subread indexes for the supplied reference .fasta file. If multiple indexes are created, the libraries will be named the ref_lib basename plus _1, _2, etc.

Examples

## Download all RefSeq reference viral genomes and make an index
download_refseq('viral', compress = FALSE)
mk_subread_index('viral.fasta')

## Download all RefSeq reference viral genomes and make more than one index
download_refseq('viral', compress = FALSE)
mk_subread_index('viral.fasta', split = .0005)

wevanjohnson/animalcules.preprocess documentation built on May 11, 2019, 8:26 p.m.