build_index: Build a index for DNA and AA mapper
In jkruppa/viralDetectTools: Modules for a viral detection pipeline

Description Usage Arguments Details Value Author(s)

The function builds a index of a small subset of sequences

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build_index(dna_set, aa_set, index_dir = NULL, index_name = NULL,
  bowtie = TRUE, pauda = TRUE, star = FALSE, force = FALSE,
  tmp_dir = tempdir())

`dna_set`	A DNAStringSet to be processed
`aa_set`	A AAStringSet to be porcessed
`index_dir`	The dir of the index (empty)
`index_name`	The name of the index
`bowtie`	Should the Bowtie2 index be build [default = TRUE]
`pauda`	Should the Pauda index be build [default = TRUE]
`star`	Should the Star index be build [default = FALSE]
`force`	Should everything be overwritten [default = FALSE]
`tmp_dir`	File path to the tmp dir

This functions calls Bowtie2, PAUDA and Star to build the DNA index. The file system is set by the function. As return the path to index files will be given.

file.list

Jochen Kruppa

jkruppa/viralDetectTools documentation built on May 30, 2019, 3:41 p.m.