oracular (1) lambda2-mkindexp.1.gz

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. Default: autodetected.

       --tmp-dir OUTPUT_DIRECTORY
              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

       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.