.TH LAMBDA_INDEXER 1 "Feb  8 2020" "lambda_indexer 1.0.2 " ""
.SH NAME
lambda_indexer \- indexer for creating lambda-compatible databases
.SH SYNOPSIS
\fBlambda_indexer\fP [\fIOPTIONS\fP] \-d DATABASE.fasta\fP
.SH 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.
.sp
Detailed information is available in the wiki: <https://github.com/seqan/lambda/wiki>
.sp
This is the indexer_binary for creating lambda-compatible databases.
.SH OPTIONS
.TP
\fB-h\fP, \fB--help\fP
Display the help message.
.TP
\fB-hh\fP, \fB--full-help\fP
Display the help message with advanced options.
.TP
\fB--version-check\fP \fIBOOL\fP
Turn this option off to disable version update notifications of the application.  One of \fI1\fP, \fION\fP, \fITRUE\fP, \fIT\fP, \fIYES\fP, \fI0\fP, \fIOFF\fP, \fIFALSE\fP, \fIF\fP, and \fINO\fP. Default: \fI1\fP.
.TP
\fB--version\fP
Display version information.
.TP
\fB--copyright\fP
Display long copyright information.
.TP
\fB-v\fP, \fB--verbosity\fP \fIINTEGER\fP
Display more/less diagnostic output during operation: 0 [only errors]; 1 [default]; 2 [+run-time, options and statistics]. In range [0..2]. Default: \fI1\fP.
.SS Input Options:
.TP
\fB-d\fP, \fB--database\fP \fIINPUT_FILE\fP
Database sequences. Valid filetypes are: \fI.sam[.*]\fP, \fI.raw[.*]\fP, \fI.gbk[.*]\fP, \fI.frn[.*]\fP, \fI.fq[.*]\fP, \fI.fna[.*]\fP, \fI.ffn[.*]\fP, \fI.fastq[.*]\fP, \fI.fasta[.*]\fP, \fI.faa[.*]\fP, \fI.fa[.*]\fP, \fI.embl[.*]\fP, and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.TP
\fB-s\fP, \fB--segfile\fP \fIINPUT_FILE\fP
SEG intervals for database(optional). Valid filetype is: \fI.seg\fP.
.SS Output Options:
.TP
\fB-di\fP, \fB--db-index-type\fP \fISTRING\fP
Suffix array or full-text minute space. One of \fIsa\fP and \fIfm\fP. Default: \fIfm\fP.
.TP
\fB--truncate-ids\fP \fISTRING\fP
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 \fIon\fP and \fIoff\fP. Default: \fIon\fP.
.SS Alphabets and Translation:
.TP
\fB-p\fP, \fB--program\fP \fISTRING\fP
Blast Operation Mode. One of \fIblastn\fP, \fIblastp\fP, \fIblastx\fP, \fItblastn\fP, and \fItblastx\fP. Default: \fIblastx\fP.
.TP
\fB-g\fP, \fB--genetic-code\fP \fIINTEGER\fP
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: \fI1\fP.
.TP
\fB-ar\fP, \fB--alphabet-reduction\fP \fISTRING\fP
Alphabet Reduction for seeding phase (ignored for BLASTN). One of \fInone\fP and \fImurphy10\fP. Default: \fImurphy10\fP.
.SS Algorithm:
.TP
\fB-a\fP, \fB--algorithm\fP \fISTRING\fP
Algorithm for SA construction (also used for FM; see Memory  Requirements below!). One of \fImergesort\fP, \fIquicksortbuckets\fP, \fIquicksort\fP, \fIradixsort\fP, and \fIskew7ext\fP. Default: \fIradixsort\fP.
.TP
\fB-t\fP, \fB--threads\fP \fIINTEGER\fP
number of threads to run concurrently (ignored if a == skew7ext).
.TP
\fB-td\fP, \fB--tmp-dir\fP \fISTRING\fP
temporary directory used by skew, defaults to working directory.
.SH REMARKS
Please see the wiki (<https://github.com/seqan/lambda/wiki>) for more information on which indexes to chose and which algorithms to pick.
.sp
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.
.SH LEGAL
\fBlambda_indexer Copyright:\fR 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
.br
\fBSeqAn Copyright:\fR 2006-2015 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
.br
\fBIn your academic works please cite:\fR Hauswedell et al (2014); doi: 10.1093/bioinformatics/btu439
.br
For full copyright and/or warranty information see \fB--copyright\fR.