Inputs and Parameters

NanoVar inputs

Mandatory postional arguments

• Long-read FASTQ/FASTA file or Mapped BAM file
• Reference genome in FASTA format (e.g. GRCH38 Human reference genome hg38)
• Working directory

Recommended arguments

• Coordinate exclusion BED file (See parameter -f below)

NanoVar options

Usage:

nanovar [-h] [-f FILTER_BED] [-l MINLEN] [-p SPLITPCT] [-a MINALIGN]
        [-b BUFFER] [-s SCORE] [-v] [-q] [-t [1-54]] [--force]
        [--mdb MDB] [--wmk WMK] [--hsb HSB]
        [long_reads] [reference_genome] [working_directory]

Example:
        nanovar -t 24 reads.fa hg38.fa ./work_dir

Positional arguments:

Parameter	Argument	Comment
[long_reads]	reads.fa	Path to long reads. Formats: fasta/fa/fa.gzip/fa.gz, fastq/fq/fq.gzip/fq.gz
[reference_genome]	hg38.fa	Path to reference genome in FASTA. Genome indexes created will overwrite indexes created by other aligners (e.g. bwa)
[working_directory]	./work_dir	Path to working directory. Directory will be created if it does not exist

Optional arguments:

Parameter	Argument	Comment
-f, --filter_bed	bed_file	BED file with genomic regions to be excluded. (e.g. telomeres and centromeres). Either specify name of in-built reference genome filter (i.e. hg38, hg19, mm10) or provide FULL path to own BED file. [None]
-l, --minlen	INT	minimum length of SV to be detected. [25]
-p, --splitpct	FLOAT	minimum percentage of unmapped bases within a long read to be considered as a split-read. 0.05<=p<=0.50 [0.05]
-a, --minalign	INT	minimum alignment length for single alignment reads. [200]
-b, --buffer	INT	nucleotide length buffer for SV breakend clustering. [50]
-s, --score	FLOAT	score threshold for defining PASS/FAIL SVs in VCF. Default score 1.0 was derived from simulated analysis. [1.0]
--mdb	mdb_path	Specify path to 'makeblastdb' executable
--wmk	wmk_path	Specify path to 'windowmasker' executable
--hsb	hsb_path	Specify path to 'hs-blastn' executable
-t, --threads	INT	number of available threads for use [1]
--force	-	run full pipeline, do not skip any redundant steps (e.g. index generation)
-q, --quiet	-	hide verbose
-h, --help	-	show this help message and exit
-v, --version	-	show version and exit