R1R2toFLASH: Run FLASH to extend paired-end reads and generate report...

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

Run FLASH to extend paired-end reads and generate report graphs.

Description

This function applies executeFLASH over R1 and R2 reads for multiple sample pools and returns a file with the extended reads for each pool.

Usage

R1R2toFLASH(runfiles, flash, min.ov = 20, max.ov = 300, err.lv = 0.1)

Arguments

runfiles	Vector including the paths of Illumina MiSeq Raw Data files, often with fastq.gz extension.
flash	File path of the FLASH executable.
min.ov	Minimum overlap (in nt) between R1 and R2 reads.
max.ov	Maximum overlap (in nt) between R1 and R2 reads.
err.lv	Mismatch fraction accepted in overlapping.

Value

The function returns a data.frame object containing FLASH results for sequenced regions.

After the execution, a fastq file with extended reads for each pool will be saved in a new folder named flash. Additionaly, two files will be saved in a reports folder:

1. FLASH_barplot.pdf: Bar plots representing extended vs not extended reads and the yield of the process for each pool.

2. FLASH_report.txt: Includes the data returned by the function with used FLASH parameters.

Author(s)

Alicia Aranda

See Also

executeFLASH

Examples

runDir <- "./run"
flash <- "./FLASH/flash.exe"
# Save the file names with complete path
runfiles<-list.files(runDir,recursive=TRUE,full.names=TRUE,include.dirs=TRUE)
min.ov <- 20
max.ov <- 300
err.lv <- 0.1
flashres <- R1R2toFLASH(runfiles,flash,min.ov,max.ov,err.lv)

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