lamassemble - Merges overlapping "long" DNA reads into a
consensus sequences
lamassemble [options] last-train.out sequences.fx
> consensus.fa
Merge DNA sequences into a consensus sequence.
- -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)