lastdb(1)
genome-scale comparison of biological sequences
Description
LASTDB
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
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-p |
interpret the sequences as proteins |
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-R |
repeat-marking options (default=10) |
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-c |
soft-mask lowercase letters |
Advanced Options (default settings)
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-Q |
input format: 0=fasta, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina (0) | ||
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-s |
volume size (unlimited) | ||
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-m |
seed pattern (non-DNA: 1) | ||
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-u |
seeding scheme (DNA: YASS) | ||
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-w |
index step (1) | ||
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-a |
user-defined alphabet | ||
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-i |
minimum limit on initial matches per query position (0) | ||
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-b |
bucket depth | ||
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-C |
child table type: 0=none, 1=byte-size, 2=short-size, 3=full (0) | ||
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-x |
just count sequences and letters | ||
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-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/