executeFLASH: Run FLASH to extend R1 and R2 reads.

In aliafdz/QApckg: Quality assessment for Miseq data derived from viral sequencing

Run FLASH to extend R1 and R2 reads.

Description

With R1 and R2 files generated by paired-end sequencing, the function executes the FLASH program to obtain the number of extended and not-extended reads.

Usage

executeFLASH(R1, R2, flash, flash.opts, outfile = "./flash.fastq")

Arguments

R1	Path for R1 reads file.
R2	Path for R2 reads file.
flash	Folder path containing the FLASH executable.
flash.opts	Character indicating FLASH options that will be part of the execution command.
outfile	File path for FLASH output. If it is not specified, the fastq file generated will be saved in the current working directory.

Value

This function returns a matrix containing the number of reads extended and not extended by FLASH. Additionaly, a fastq file with extended reads will be saved to outfile path. Further FLASH output files will be saved in a new folder named "tmp".

Note

This function is defined for correct execution of R1R2toFLASH function from the same package, where all arguments are defined automatically.

Author(s)

Alicia Aranda

See Also

R1R2toFLASH

aliafdz/QApckg documentation built on June 2, 2022, 10:29 a.m.