Man page - lamassemble(1)

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Package: lamassemble
apt-get install lamassemble

Manuals in package:

Documentations in package:

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)