ngmlr - CoNvex Gap-cost alignMents for Long Reads

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.

ngmlr 0.2.7                                         June 2020                                           NGMLR(1)

       Ngmlr is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference
       genomes.  It  was  designed  to quickly and correctly align the reads, including those spanning (complex)
       structural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping  locations  for  a
       read  and  then a banded Smith- Waterman alignment algorithm to compute the final alignment. Ngmlr uses a
       convex gap cost model that penalizes gap extensions for longer gaps less than for shorter ones to compute
       precise alignments.

       ngmlr - CoNvex Gap-cost alignMents for Long Reads

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]

ngmlr [options] -r<reference>-q<reads> [-o<output>]