unicycler_align1

Usage

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)