.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.5.
.TH LAMASSEMBLE "1" "July 2022" "lamassemble 1.4.2" "User Commands"
.SH NAME
lamassemble \- Merges overlapping "long" DNA reads into a consensus sequences
.SH SYNOPSIS
.B lamassemble
[\fI\,options\/\fR] \fI\,last-train.out sequences.fx > consensus.fa\/\fR
.SH DESCRIPTION
Merge DNA sequences into a consensus sequence.
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-a\fR, \fB\-\-alignment\fR
print an alignment, not a consensus
.TP
\fB\-c\fR, \fB\-\-consensus\fR
just make a consensus, of already\-aligned sequences
.TP
\fB\-g\fR G, \fB\-\-gap\-max\fR=\fI\,G\/\fR
use alignment columns with <= G% gaps (default=50)
.TP
\fB\-\-end\fR
\&... including gaps past the ends of the sequences
.TP
\fB\-s\fR S, \fB\-\-seq\-min\fR=\fI\,S\/\fR
omit consensus flanks with < S sequences (default=1)
.TP
\fB\-n\fR NAME, \fB\-\-name\fR=\fI\,NAME\/\fR
name of the consensus sequence (default=lamassembled)
.TP
\fB\-o\fR BASE, \fB\-\-out\fR=\fI\,BASE\/\fR
just write MAFFT input files, named BASE.xxx
.TP
\fB\-p\fR P, \fB\-\-prob\fR=\fI\,P\/\fR
use pairwise restrictions with error probability <= P
(default=0.002)
.TP
\fB\-d\fR D, \fB\-\-diagonal\-max\fR=\fI\,D\/\fR
max change in alignment diagonal between pairwise
alignments (default=1000)
.TP
\fB\-v\fR, \fB\-\-verbose\fR
show progress messages
.TP
\fB\-\-all\fR
use all of each sequence, not just aligning part
.TP
\fB\-\-mafft\fR=\fI\,ARGS\/\fR
additional arguments for MAFFT
.IP
LAST options:
.TP
\fB\-P\fR P
number of parallel threads (default=1)
.TP
\fB\-W\fR W
use minimum positions in length\-W windows (default=19)
.TP
\fB\-m\fR M
max initial matches per query position (default=5)
.TP
\fB\-z\fR Z
max gap length (default=30)