.TH LAMBDA2_MKINDEXP 1 "Dec  7 2020" "lambda2 mkindexp 2.0.0" ""
.SH NAME
lambda2_mkindexp \- the Local Aligner for Massive Biological DatA
.SH SYNOPSIS
\fBlambda2 mkindexp\fP [\fIOPTIONS\fP] \-d DATABASE.fasta [-i INDEX.lambda]\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.
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Detailed information is available in the wiki: <https://github.com/seqan/lambda/wiki>
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This is the indexer_binary for creating lambda-compatible databases.
.SH OPTIONS
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\fB-h\fP, \fB--help\fP
Display the help message.
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\fB-hh\fP, \fB--full-help\fP
Display the help message with advanced options.
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\fB--version\fP
Display version information.
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\fB--copyright\fP
Display long copyright information.
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\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:
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\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.
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\fB-m\fP, \fB--acc-tax-map\fP \fIINPUT_FILE\fP
An NCBI or UniProt accession-to-taxid mapping file. Download from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/ or ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/ . Valid filetypes are: \fI.dat[.*]\fP and \fI.accession2taxid[.*]\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
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\fB-x\fP, \fB--tax-dump-dir\fP \fIINPUT_DIRECTORY\fP
A directory that contains nodes.dmp and names.dmp; unzipped from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
.SS Output Options:
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\fB-i\fP, \fB--index\fP \fIOUTPUT_DIRECTORY\fP
The output directory for the index files (defaults to "DATABASE.lambda"). Valid filetype is: \fI.lambda\fP.
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\fB--db-index-type\fP \fISTRING\fP
Suffix array or full-text minute space. One of \fIfm\fP and \fIbifm\fP. Default: \fIfm\fP.
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\fB--truncate-ids\fP \fIBOOL\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 \fI1\fP, \fION\fP, \fITRUE\fP, \fIT\fP, \fIYES\fP, \fI0\fP, \fIOFF\fP, \fIFALSE\fP, \fIF\fP, and \fINO\fP. Default: \fIon\fP.
.SS Alphabets and Translation:
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\fB-a\fP, \fB--input-alphabet\fP \fISTRING\fP
Alphabet of the database sequences (specify to override auto-detection); if input is Dna, it will be translated. One of \fIauto\fP, \fIdna5\fP, and \fIaminoacid\fP. Default: \fIauto\fP.
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\fB-g\fP, \fB--genetic-code\fP \fIINTEGER\fP
The translation table to use if input is Dna. See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c for ids (default is generic). Default: \fI1\fP.
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\fB-r\fP, \fB--alphabet-reduction\fP \fISTRING\fP
Alphabet Reduction for seeding phase. One of \fInone\fP and \fImurphy10\fP. Default: \fImurphy10\fP.
.SS Algorithm:
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\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.
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\fB-t\fP, \fB--threads\fP \fIINTEGER\fP
number of threads to run concurrently. Default: autodetected.
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\fB--tmp-dir\fP \fIOUTPUT_DIRECTORY\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.
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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
\fBlambda2 mkindexp Copyright:\fR 2013-2019 Hannes Hauswedell, released under the GNU AGPL v3 (or later); 2016-2019 Knut Reinert and Freie Universität Berlin, released under the 3-clause-BSDL
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\fBSeqAn Copyright:\fR 2006-2015 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
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\fBIn your academic works please cite:\fR Hauswedell et al (2014); doi: 10.1093/bioinformatics/btu439
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For full copyright and/or warranty information see \fB--copyright\fR.