Command Line Interface

Options

./hpg-aligner {dna | rna | bs} -i|--fq|--fastq=<file> -b|--bwt-index=<file> [-g|--genome-ref=<file>] [--report-all] [-m|--match-output=<file>] [--gpu-threads=<int>] [--cpu-threads=<int>] [--rna-seq] [--cal-seeker-errors=<int>] [--min-cal-size=<int>] [--max-distance-seeds=<int>] [--read-batch-size=<int>] [--write-batch-size=<int>] [--num-cal-seekers=<int>] [--num-sw-servers=<int>] [--num-bwt-threads=<int>] [--num-region-threads=<int>] [--seed-size=<int>] [--min-seed-size=<int>] [--cal-flank-length=<int>] [--match=<double>] [--mismatch=<double>] [--gap-open=<double>] [--gap-extend=<double>] [--min-sw-score=<double>] [--max-intron-length=<int>] [--min-intron-length=<int>] [-t|--timing] [-s|--statistics] [-h|--help] [--splice-exact=<file>] [--splice-extend=<file>] [-j|--fq2|--fastq2=<file>] [--pair-mode=<int>] [--pair-min-distance=<int>] [--pair-max-distance=<int>] [--report-n-best=<int>] [--report-n-hits=<int>] [--min-num-seeds=<int>] [--max-num-seeds=<int>] [--gpu-enable]
-i, --fq, --fastq=<file> Reads file input
-b, --bwt-index=<file> BWT directory name
-g, --genome-ref=<file> Genome filename
--report-all Report all alignments
-m, --match-output=<file> Match output filename
--gpu-threads=<int> Number of GPU Threads
--cpu-threads=<int> Number of CPU Threads
--rna-seq Enable RNA Seq
--cal-seeker-errors=<int> Number of errors in CAL Seeker
--min-cal-size=<int> Minimum CAL size
--max-distance-seeds=<int> Maximum distance between seeds
--read-batch-size=<int> Batch Size
--write-batch-size=<int> Write Size
--num-cal-seekers=<int> Number of CAL Seekers
--num-sw-servers=<int> Number of Smith-Waterman servers
--num-bwt-threads=<int> Number of BWT threads
--num-region-threads=<int> Number of region threads
--seed-size=<int> Number of nucleotides in a seed
--min-seed-size=<int> Minimum number of nucleotides in a seed
--cal-flank-length=<int> Flank length for CALs
--match=<double> Match value for Smith-Waterman algorithm
--mismatch=<double> Mismatch value for Smith-Waterman algorithm
--gap-open=<double> Gap open penalty for Smith-Waterman algorithm
--gap-extend=<double> Gap extend penalty for Smith-Waterman algorithm
--min-sw-score=<double> Minimum score for valid mappings
--max-intron-length=<int> Maximum intron length
--min-intron-length=<int> Minimum intron length
-t, --timing Timming mode active
-s, --statistics Statistics mode active
-h, --help Help option
--splice-exact=<file> Splice Junctions exact filename
--splice-extend=<file> Splice Junctions extend filename
-j, --fq2, --fastq2=<file> Reads file input #2 (for paired mode)
--pair-mode=<int> Pair mode: 0 = single-end, 1 = paired-end, 2 = mate-pair
--pair-min-distance=<int> Minimum distance between pairs
--pair-max-distance=<int> Maximum distance between pairs
--report-n-best=<int> Report the <n> best alignments
--report-n-hits=<int> Report <n> hits
--min-num-seeds=<int> Minimum number of seeds per read
--max-num-seeds=<int> Maximum number of seeds per read
--gpu-enable Enable GPU Process