The source code of the Aryana next generation sequencing (NGS) aligner.
Download Aryana from github and run "make"
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