Input/Output:

-r <file>, --reference <file>

(required)

Path to the reference genome (FASTA/Q, can be gzipped)

-q <file>, --query <file>

Path to the read file (FASTA/Q) [/dev/stdin]

-o <string>, --output <string>

Adds RG:Z:<string> to all alignments in SAM/BAM [none]

--skip-write

Don't write reference index to disk [false]

--bam-fix

Report reads with > 64k CIGAR operations as unmapped. Required to be compatibel to BAM format [false]

--rg-id <string>

Adds RG:Z:<string> to all alignments in SAM/BAM [none]

--rg-sm <string>

RG header: Sample [none]

--rg-lb <string>

RG header: Library [none]

--rg-pl <string>

RG header: Platform [none]

--rg-ds <string>

RG header: Description [none]

--rg-dt <string>

RG header: Date (format: YYYY-MM-DD) [none]

--rg-pu <string>

RG header: Platform unit [none]

--rg-pi <string>

RG header: Median insert size [none]

--rg-pg <string>

RG header: Programs [none]

--rg-cn <string>

RG header: sequencing center [none]

--rg-fo <string>

RG header: Flow order [none]

--rg-ks <string>

RG header: Key sequence [none]

General:

-t <int>, --threads <int>

Number of threads [1]

-x <pacbio, ont>, --presets <pacbio, ont>

Parameter presets for different sequencing technologies [pacbio]

-i <0-1>, --min-identity <0-1>

Alignments with an identity lower than this threshold will be discarded [0.65]

-R <int/float>, --min-residues <int/float>

Alignments containing less than <int> or (<float> * read length) residues will be discarded [0.25]

--no-smallinv

Don't detect small inversions [false]

--no-lowqualitysplit

Split alignments with poor quality [false]

--verbose

Debug output [false]

--no-progress

Don't print progress info while mapping [false]

Advanced:

--match <float>

Match score [2]

--mismatch <float>

Mismatch score [-5]

--gap-open <float>

Gap open score [-5]

--gap-extend-max <float>

Gap open extend max [-5]

--gap-extend-min <float>

Gap open extend min [-1]

--gap-decay <float>

Gap extend decay [0.15]

-k <10-15>, --kmer-length <10-15>

K-mer length in bases [13]

--kmer-skip <int>

Number of k-mers to skip when building the lookup table from the reference [2]

--bin-size <int>

Sets the size of the grid used during candidate search [4]

--max-segments <int>

Max number of segments allowed for a read per kb [1]

--subread-length <int>

Length of fragments reads are split into [256]

--subread-corridor <int>

Length of corridor sub-reads are aligned with [40]