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)