lamassemble1
Merges overlapping "long" dna reads into a consensus sequences
Usage
lamassemble [options]
last-train.out
sequences.fx
>
consensus.fa
Overview
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)
Releases
Unchanged in 2 releases since Debian 12 (Bookworm).