lambda_indexer - indexer for creating lambda-compatible
databases
lambda_indexer [OPTIONS] -d
DATABASE.fasta
Lambda is a local aligner optimized for many query sequences and
searches in protein space. It is compatible to BLAST, but much faster than
BLAST and many other comparable tools.
Detailed information is available in the wiki:
<https://github.com/seqan/lambda/wiki>
This is the indexer_binary for creating lambda-compatible
databases.
- -h, --help
- Display the help message.
- -hh,
--full-help
- Display the help message with advanced options.
- --version-check
BOOL
- Turn this option off to disable version update notifications of the
application. One of 1, ON, TRUE, T,
YES, 0, OFF, FALSE, F, and NO.
Default: 1.
- --version
- Display version information.
- --copyright
- Display long copyright information.
- -v, --verbosity
INTEGER
- Display more/less diagnostic output during operation: 0 [only errors]; 1
[default]; 2 [+run-time, options and statistics]. In range [0..2].
Default: 1.
- -d, --database
INPUT_FILE
- Database sequences. Valid filetypes are: .sam[.*], .raw[.*],
.gbk[.*], .frn[.*], .fq[.*], .fna[.*],
.ffn[.*], .fastq[.*], .fasta[.*], .faa[.*],
.fa[.*], .embl[.*], and .bam, where * is any of the
following extensions: gz, bz2, and bgzf for
transparent (de)compression.
- -s, --segfile
INPUT_FILE
- SEG intervals for database(optional). Valid filetype is: .seg.
- -di, --db-index-type
STRING
- Suffix array or full-text minute space. One of sa and fm.
Default: fm.
- --truncate-ids
STRING
- Truncate IDs at first whitespace. This saves a lot of space and is
irrelevant for all LAMBDA output formats other than BLAST Pairwise (.m0).
One of on and off. Default: on.
- -p, --program
STRING
- Blast Operation Mode. One of blastn, blastp, blastx,
tblastn, and tblastx. Default: blastx.
- -g, --genetic-code
INTEGER
- The translation table to use (not for BlastN, BlastP). See
https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c for ids
(default is generic). Default: 1.
- -ar,
--alphabet-reduction STRING
- Alphabet Reduction for seeding phase (ignored for BLASTN). One of
none and murphy10. Default: murphy10.
- -a, --algorithm
STRING
- Algorithm for SA construction (also used for FM; see Memory Requirements
below!). One of mergesort, quicksortbuckets,
quicksort, radixsort, and skew7ext. Default:
radixsort.
- -t, --threads
INTEGER
- number of threads to run concurrently (ignored if a == skew7ext).
- -td, --tmp-dir
STRING
- temporary directory used by skew, defaults to working directory.
Please see the wiki (<https://github.com/seqan/lambda/wiki>)
for more information on which indexes to chose and which algorithms to
pick.
Note that the indexes created are binary and not compatible
between different CPU endiannesses. Also the on-disk format is still subject
to change between Lambda versions.
lambda_indexer Copyright: 2013-2017 Hannes Hauswedell,
released under the GNU GPL v3 (or later); 2016-2017 Knut Reinert and Freie
Universität Berlin, released under the 3-clause-BSDL
SeqAn Copyright: 2006-2015 Knut Reinert, FU-Berlin; released under the
3-clause BSDL.
In your academic works please cite: Hauswedell et al (2014); doi:
10.1093/bioinformatics/btu439
For full copyright and/or warranty information see --copyright.