Scroll to navigation

LAMBDA_INDEXER(1) LAMBDA_INDEXER(1)

NAME

lambda_indexer - indexer for creating lambda-compatible databases

SYNOPSIS

lambda_indexer [OPTIONS] -d DATABASE.fasta

DESCRIPTION

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.

OPTIONS

-h, --help
Display the help message.
-hh, --full-help
Display the help message with advanced options.
--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.

Input Options:

-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.

Output Options:

-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.

Alphabets and Translation:

-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.

Algorithm:

-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.

REMARKS

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.

LEGAL

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.
Jan 21 2017 lambda_indexer 1.0.1