remove_reference: Removes sequence that map to a given reference.

In Gibbons-Lab/mbtools: Provides helper functions for microbiome preprocessing and analysis

Removes sequence that map to a given reference.

Description

This can be used for a variety of applications the most common ones are:

• removing sequences from the host

• removing ribosomal sequences

• removing contaminants

This function uses minimap2 to align and identify hits and does not require a prebuilt index.

Usage

remove_reference(reads, out, reference, alignments = NA, threads = 3)

Arguments

reads	A character vector containing the read files in fastq format. Can be generated using find_read_files.
out	A folder to which to save the filtered fastq files.
reference	Path to a fasta file (can be gzipped) that contains the sequences to filter. Can be a genome or transcripts.
alignments	Whether to keep the alignment. If not NA should be a string indicating the path to the output bam file.
threads	How many threads to use for mapping.

Value

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

Examples

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Gibbons-Lab/mbtools documentation built on Jan. 28, 2024, 11:08 a.m.