get_phix_genome: Download genome (fasta), annotation (GTF) and contaminants
In ORFik: Open Reading Frames in Genomics

Description Usage Arguments Details Value See Also Examples

This function automatically downloads (if files not already exists) genomes and contaminants specified for genome alignment. Will create a R transcript database (TxDb object) from the annotation.
It will also index the genome for you
If you misspelled something or crashed, delete wrong files and run again.
Do remake = TRUE, to do it all over again.

1	get_phix_genome(phix, output.dir, gunzip)

`phix`	logical, default FALSE, download phix sequence to filter out with. Phix is used as a contaminant genome. Only use if illumina sequencing. Phix is used in Illumina sequencers for sequencing quality control. Genome is: refseq, Escherichia virus phiX174
`output.dir`	directory to save downloaded data
`gunzip`	logical, default TRUE, uncompress downloaded files that are zipped when downloaded, should be TRUE!

If you want custom genome or gtf from you hard drive, assign it after you run this function, like this:
annotation <- getGenomeAndAnnotation(GTF = FALSE, genome = FALSE)
annotation["genome"] = "path/to/genome.fasta"
annotation["gtf"] = "path/to/gtf.gtf"

a named character vector of path to genomes and gtf downloaded, and additional contaminants if used. If merge_contaminants is TRUE, will not give individual fasta files to contaminants, but only the merged one.

Other STAR: STAR.align.folder(), STAR.align.single(), STAR.allsteps.multiQC(), STAR.index(), STAR.install(), STAR.multiQC(), STAR.remove.crashed.genome(), install.fastp()

output.dir <- "/Bio_data/references/zebrafish"
#getGenomeAndAnnotation("Danio rerio", output.dir)

## Get Phix contamints to deplete during alignment
#getGenomeAndAnnotation("Danio rerio", output.dir, phix = TRUE)