NAME
lamassemble - Merges overlapping "long" DNA reads into a consensus sequences
SYNOPSIS
lamassemble [options] last-train.out sequences.fx > consensus.fa
DESCRIPTION
Merge DNA sequences into a consensus sequence.
OPTIONS
- -h, --help
-
show this help message and exit
- -a, --alignment
-
print an alignment, not a consensus
- -c, --consensus
-
just make a consensus, of already-aligned sequences
- -g G, --gap-max=G
-
use alignment columns with <= G% gaps (default=50)
- --end
-
... including gaps past the ends of the sequences
- -s S, --seq-min=S
-
omit consensus flanks with < S sequences (default=1)
- -n NAME, --name=NAME
-
name of the consensus sequence (default=lamassembled)
- -o BASE, --out=BASE
-
just write MAFFT input files, named BASE.xxx
- -p P, --prob=P
-
use pairwise restrictions with error probability <= P (default=0.002)
- -d D, --diagonal-max=D
-
max change in alignment diagonal between pairwise alignments (default=1000)
- -v, --verbose
-
show progress messages
- --all
-
use all of each sequence, not just aligning part
- --mafft=ARGS
-
additional arguments for MAFFT
-
LAST options:
- -P P
-
number of parallel threads (default=1)
- -W W
-
use minimum positions in length-W windows (default=19)
- -m M
-
max initial matches per query position (default=5)
- -z Z
-
max gap length (default=30)