.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
.TH LASTDB "1" "December 2015" "lastdb 712" "User Commands"
.SH NAME
lastdb \- genome-scale comparison of biological sequences
.SH SYNOPSIS
.B lastdb
[\fI\,options\/\fR] \fI\,output-name fasta-sequence-file(s)\/\fR
.SH DESCRIPTION
Prepare sequences for subsequent alignment with lastal.
.SH OPTIONS
.SS Main Options
.TP
\fB\-h\fR, \fB\-\-help\fR
show all options and their default settings, and exit
.TP
\fB\-p\fR
interpret the sequences as proteins
.TP
\fB\-R\fR
repeat\-marking options (default=10)
.TP
\fB\-c\fR
soft\-mask lowercase letters
.SS Advanced Options (default settings)
.TP
\fB\-Q\fR
input format: 0=fasta, 1=fastq\-sanger, 2=fastq\-solexa, 3=fastq\-illumina (0)
.TP
\fB\-s\fR
volume size (unlimited)
.TP
\fB\-m\fR
seed pattern (non\-DNA: 1)
.TP
\fB\-u\fR
seeding scheme (DNA: YASS)
.TP
\fB\-w\fR
index step (1)
.TP
\fB\-a\fR
user\-defined alphabet
.TP
\fB\-i\fR
minimum limit on initial matches per query position (0)
.TP
\fB\-b\fR
bucket depth
.TP
\fB\-C\fR
child table type: 0=none, 1=byte\-size, 2=short\-size, 3=full (0)
.TP
\fB\-x\fR
just count sequences and letters
.TP
\fB\-v\fR
be verbose: write messages about what lastdb is doing
.TP
\fB\-V\fR, \fB\-\-version\fR
show version information, and exit
.SH "REPORTING BUGS"
Report bugs to: last\-align@googlegroups.com
.br
LAST home page: http://last.cbrc.jp/