saditya88/ngsalign repository overview

usage: ngsalign [-h] --ngs NGS --ref REF --fq FQ [FQ ...] [--threads THREADS] [--bwa]

Input parameters and files for processing.

optional arguments: -h, --help show this help message and exit --ngs NGS, -n NGS Short reads: sr; ONT: on; PacBio: pb --ref REF, -r REF The reference sequence in FASTA format --fq FQ [FQ ...], -f FQ [FQ ...] Sample FASTQ files --threads THREADS, -t THREADS Number of CPU threads to use (Auto default: 15) --bwa, -b Optional: In case you wish to use BWA-MEM for short reads