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.