lastdb1
Genome-scale comparison of biological sequences
Usage
lastdb [options]
output-name
fasta-sequence-file(s)
Overview
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
Releases
8 releases since Debian 6.0 (Squeeze); the text changed 3 times.
--help since Debian 9 (Stretch);
--version since Debian 9 (Stretch);
-C since Debian 9 (Stretch);
-Q since Debian 9 (Stretch);
-R since Debian 9 (Stretch);
-V since Debian 9 (Stretch);
-a since Debian 9 (Stretch);
-b since Debian 9 (Stretch);
-c since Debian 9 (Stretch);
-h since Debian 9 (Stretch);
-i since Debian 9 (Stretch);
-m since Debian 9 (Stretch);
-p since Debian 9 (Stretch);
-s since Debian 9 (Stretch);
-u since Debian 9 (Stretch);
-v since Debian 9 (Stretch);
-w since Debian 9 (Stretch);
-x since Debian 9 (Stretch).