milad621 / src

The source code of the Aryana next generation sequencing (NGS) aligner

src

The source code of the Aryana next generation sequencing (NGS) aligner.

Installation

Download Aryana from github and run "make"

Running Aryana

Alignment of single end reads

./aryana [-x human_g1k_v37.fasta] [-U reads.fastq]

-p INT	Number of threads

-P INT	Number of potential candidates to select for more precise alignment

--seed INT	Fixed length for the seeds

Alignment of paired end reads

./aryana [-x human_g1k_v37.fasta] [-1 pair1.fastq] [-2 pair2.fastq] --{fr, ff, rf} -I min -X max

--fr/--ff/--rf	Refers to orientation of the pairs. /forward-reverse/forward-forward/reverse-forward

-I INT	Minimum insert size

-X INT	Maximum insert size