AlleleProfileR.merge: Merge paired-end reads

In abruyneel/AlleleProfileR: Genome editing strategy agnostic variant identification and profiling tool

Description

Merge peared end reads using PEAR, FLASH or fastq-join. This external software needs to be installed manually and needs to be addressable from the terminal.

Usage

AlleleProfileR.merge(files, method = "pear", params = "-v 10",
  subset = NULL)

Arguments

files	Vector with files. Output of AlleleProfileR.read.folders
method	Merge method, options are pear, fastq-join or flash. Default is pear (PEAR).
params	String with additional parameters
subset	Vector with the indices of the entries that should be processed. Default is NULL, all entries will be analyzed.

Author(s)

Arne Bruyneel

References

• Zhang, J., et al. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 2014;30(5):614-620.

• Magoč, T. and Salzberg, S.L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 2011;27(21):2957-2963.

• Aronesty, E. Comparison of Sequencing Utility Programs. The Open Bioinformatics Journal 2013;7:1-8.

abruyneel/AlleleProfileR documentation built on June 12, 2020, 2:47 p.m.