Removes sequence contamination from another target organism (for instance human sequences).

This function uses bowtie2 to align and identify hits. This requires a pre-built index, for instance by using download_index.

remove_organism(reads, index = NA, out, organism = "hg19",
  where = "./bowtie2")

Arguments

reads	A character vector containing the read files in fastq format.
index	Additional barcode file that should be filtered as well.
out	A folder to which to save the filtered fastq files.
organism	The base name for the index. Defaults to human (hg19).
where	Where to find the previously generated index files.

A numeric vector with two entries. The number of sequences after filtering (non-human), and the number of removed sequences (human).

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