lastdb(1) genome-scale comparison of biological sequences


lastdb [,options/] ,output-name fasta-sequence-file(s)/


Prepare sequences for subsequent alignment with lastal.


Main Options

-h, --help
show all options and their default settings, and exit
interpret the sequences as proteins
repeat-marking options (default=10)
soft-mask lowercase letters

Advanced Options (default settings)

input format: 0=fasta, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina (0)
volume size (unlimited)
seed pattern (non-DNA: 1)
seeding scheme (DNA: YASS)
index step (1)
user-defined alphabet
minimum limit on initial matches per query position (0)
bucket depth
child table type: 0=none, 1=byte-size, 2=short-size, 3=full (0)
just count sequences and letters
be verbose: write messages about what lastdb is doing
-V, --version
show version information, and exit


Report bugs to: [email protected]
LAST home page: