gapremove: Removing gap-rich positions and/or reads/sequences

In longreadvqs: Viral Quasispecies Comparison from Long-Read Sequencing Data

Removing gap-rich positions and/or reads/sequences

Description

Removes nucleotide positions (vertical) and/or reads/sequences (horizontal) that contain gaps more than the specified cut-off percentage from the alignment.

Usage

gapremove(fasta, vgappct = 70, hgappct = 70, fastaname = "filteredfast.fasta")

Arguments

fasta	Input as a read or multiple sequence alignment in FASTA format
vgappct	The percent cut-off of vertical gap (-), i.e., if a position in the alignment has %gap >= vgappct, that position will be removed.
hgappct	The percent cut-off of horizontal gap (-), i.e., if a sequence or read in the alignment has %gap >= hgappct, that sequence or read will be removed.
fastaname	Output file name in FASTA format

Value

FASTA read or multiple sequence alignment written out to the input directory

Examples

## Locate input FASTA file-------------------------------------------------------------------------
fastafilepath <- system.file("extdata", "gaprichfast.fasta", package = "longreadvqs")

## Indicate output directory and file name---------------------------------------------------------
outfast <- tempfile()

## Remove positions with gap >= 60% and reads/sequences with gap >= 10%----------------------------
gapremove(fastafilepath, vgappct = 60, hgappct = 10, fastaname = outfast)

longreadvqs documentation built on Sept. 11, 2024, 6:29 p.m.