NAME

       lambda2 mkindexp - the Local Aligner for Massive Biological DatA

SYNOPSIS

       lambda2 mkindexp [OPTIONS] -d DATABASE.fasta [-i INDEX.lambda]

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.

       -m, --acc-tax-map INPUT_FILE
              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: .dat[.*] and .accession2taxid[.*], where *  is  any  of  the
              following extensions: gz, bz2, and bgzf for transparent (de)compression.

       -x, --tax-dump-dir INPUT_DIRECTORY
              A    directory    that    contains   nodes.dmp   and   names.dmp;   unzipped   from
              ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz

   Output Options:
       -i, --index OUTPUT_DIRECTORY
              The output directory for the index files  (defaults  to  "DATABASE.lambda").  Valid
              filetype is: .lambda.

       --db-index-type STRING
              Suffix array or full-text minute space. One of fm and bifm. Default: fm.

       --truncate-ids BOOL
              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 1, ON,  TRUE,  T,
              YES, 0, OFF, FALSE, F, and NO. Default: on.

   Alphabets and Translation:
       -a, --input-alphabet STRING
              Alphabet  of  the database sequences (specify to override auto-detection); if input
              is Dna, it will be translated. One of auto, dna5, and aminoacid. Default: auto.

       -g, --genetic-code INTEGER
              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: 1.

       -r, --alphabet-reduction STRING
              Alphabet Reduction for seeding phase. One of none and murphy10. Default: murphy10.

   Algorithm:
       --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). In range [1..40].
              Default: 4.

       --tmp-dir OUTPUT_DIRECTORY
              temporary   directory  used  by  skew,  defaults  to  working  directory.  Default:
              /build/lambda-align2-_d4I_T/lambda-align2-2.0.0/build/src.

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

       lambda2 mkindexp Copyright: 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
       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.