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-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.

   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.