filtfast: Filtering highly dissimilar reads/sequences out of the...

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

Filtering highly dissimilar reads/sequences out of the alignment

Description

Removes reads/sequences of which Hamming similarity to the consensus of all reads/sequences in the alignment is less than the specified quantile (qt) of the similarity distribution.

Usage

filtfast(fasta, qt = 0.25, fastaname = "filteredfast.fasta")

Arguments

fasta	Input as a read or multiple sequence alignment in FASTA format
qt	If Hamming similarity score of a read/sequence to the consensus of all reads/sequences is less than the specified quantile (qt) of the similarity distribution, that read/sequence 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", "dissimfast.fasta", package = "longreadvqs")

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

## Remove reads/sequences that the similarity < 1st quartile (0.25 quantile)-----------------------
filtfast(fastafilepath, qt = 0.25, fastaname = outfast)

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