NAME

       ngmlr - CoNvex Gap-cost alignMents for Long Reads

SYNOPSIS

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

DESCRIPTION

       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.

OPTIONS

   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]

AUTHOR

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