lastdb(1)
genome-scale comparison of biological sequences
SYNOPSIS
lastdb
[,options/] ,output-name fasta-sequence-file(s)/
DESCRIPTION
Prepare sequences for subsequent alignment with lastal.
OPTIONS
Main Options
- -h, --help
-
show all options and their default settings, and exit
- -p
-
interpret the sequences as proteins
- -R
-
repeat-marking options (default=10)
- -c
-
soft-mask lowercase letters
Advanced Options (default settings)
- -Q
-
input format: 0=fasta, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina (0)
- -s
-
volume size (unlimited)
- -m
-
seed pattern (non-DNA: 1)
- -u
-
seeding scheme (DNA: YASS)
- -w
-
index step (1)
- -a
-
user-defined alphabet
- -i
-
minimum limit on initial matches per query position (0)
- -b
-
bucket depth
- -C
-
child table type: 0=none, 1=byte-size, 2=short-size, 3=full (0)
- -x
-
just count sequences and letters
- -v
-
be verbose: write messages about what lastdb is doing
- -V, --version
-
show version information, and exit
