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.