table of contents
other versions
- bullseye 1179-1+b1
- testing 1420-1
- unstable 1447-1
- experimental 1420-2~0exp
| LASTDB(1) | User Commands | LASTDB(1) |
NAME¶
lastdb - 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
REPORTING BUGS¶
Report bugs to: last-align@googlegroups.com
LAST home page: http://last.cbrc.jp/
| December 2015 | lastdb 712 |