NAME

       unicycler_align - sensitive semi-global long read aligner

SYNOPSIS

       unicycler_align  [-h]  --ref  REF  --reads READS --sam SAM [--contamination CONTAMINATION]
       [--scores  SCORES]  [--low_score  LOW_SCORE]  [--keep_bad]   [--sensitivity   SENSITIVITY]
       [--threads   THREADS]   [--verbosity  VERBOSITY]  [--min_len  MIN_LEN]  [--allowed_overlap
       ALLOWED_OVERLAP]

DESCRIPTION

       Unicycler align - a sensitive semi-global long read aligner

OPTIONS

       -h, --help
              show this help message and exit

       --ref REF
              FASTA file containing one or more reference sequences

       --reads READS
              FASTQ or FASTA file of long reads

       --sam SAM
              SAM file of resulting alignments

       --contamination CONTAMINATION
              FASTA file of known contamination in long reads

       --scores SCORES
              Comma-delimited string of alignment scores: match, mismatch, gap open,  gap  extend
              (default: 3,-6,-5,-2)

       --low_score LOW_SCORE
              Score threshold - alignments below this are considered poor (default: set threshold
              automatically)

       --keep_bad
              Include alignments in the results even if they are below the  low  score  threshold
              (default: low-scoring alignments are discarded)

       --sensitivity SENSITIVITY
              A number from 0 (least sensitive) to 3 (most sensitive) (default: 0)

       --threads THREADS
              Number of threads used (default: number of CPUs, up to 8)

       --verbosity VERBOSITY
              Level of stdout information (0 to 4) (default: 1)

       --min_len MIN_LEN
              Minimum  alignment  length  (bp)  -  exclude  alignments  shorter  than this length
              (default: 100)

       --allowed_overlap ALLOWED_OVERLAP
              Allow this much overlap between alignments in a single read (default: 100)

SEE ALSO

       unicycler(1)

AUTHOR

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