unicycler_align1
Sensitive semi-global long read aligner
Usage
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]
Overview
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)