NAME

       lambda2 searchn - the Local Aligner for Massive Biological DatA

SYNOPSIS

       lambda2 searchn [OPTIONS] -q QUERY.fasta -i INDEX.lambda [-o output.m8]

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>

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:
       -q, --query INPUT_FILE
              Query 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.

       -i, --index INPUT_DIRECTORY
              The  database  index (created by the 'lambda mkindexn' command). Valid filetype is:
              .lambda.

   Output Options:
       -o, --output OUTPUT_FILE
              File to hold reports on hits (.m* are blastall -m* formats; .m8  is  tab-seperated,
              .m9  is  tab-seperated with with comments, .m0 is pairwise format). Valid filetypes
              are: .sam[.*], .m9[.*], .m8[.*], .m0[.*], and .bam, where * is any of the following
              extensions: gz, bz2, and bgzf for transparent (de)compression. Default: output.m8.

       --output-columns STRING
              Print  specified  column  combination and/or order (.m8 and .m9 outputs only); call
              -oc help for more details. Default: std.

       --percent-identity INTEGER
              Output only matches above this threshold (checked before e-value check).  In  range
              [0..100]. Default: 0.

       -e, --e-value DOUBLE
              Output  only  matches  that score below this threshold. In range [0..100]. Default:
              1e-04.

       -n, --num-matches INTEGER
              Print at most this number of matches per query. In range [1..10000]. Default: 256.

       --sam-with-refheader BOOL
              BAM files require all subject names to be written to the header. For  SAM  this  is
              not  required, so Lambda does not automatically do it to save space (especially for
              protein database this is a lot!). If you still want them with SAM, e.g. for  better
              BAM  compatibility,  use this option. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F,
              and NO. Default: off.

       --sam-bam-seq STRING
              Write matching DNA subsequence into SAM/BAM file. If set to uniq than the  sequence
              is  omitted iff it is identical to the previous match's subsequence. One of always,
              uniq, and never. Default: uniq.

       --sam-bam-tags STRING
              Write the specified optional columns to the SAM/BAM file. Call --sam-bam-tags  help
              for more details. Default: AS NM ae ai qf.

       --sam-bam-clip STRING
              Whether to hard-clip or soft-clip the regions beyond the local match. Soft-clipping
              retains the full sequence in the output file, but obviously uses more space. One of
              hard and soft. Default: hard.

   General Options:
       -t, --threads INTEGER
              number of threads to run concurrently. In range [1..40]. Default: 4.

   Seeding / Filtration:
       --adaptive-seeding BOOL
              Grow  the seed if it has too many hits (low complexity filter). One of 1, ON, TRUE,
              T, YES, 0, OFF, FALSE, F, and NO. Default: off.

       --seed-length INTEGER
              Length of the seeds. In range [3..50]. Default: 14.

       --seed-offset INTEGER
              Offset for seeding (if unset = seed-length/2). In range [1..50]. Default: 7.

       --seed-delta INTEGER
              maximum seed distance. In range [0..1]. Default: 1.

       --seed-delta-increases-length BOOL
              Seed delta increases the min. seed length (for affected seeds). One of 1, ON, TRUE,
              T, YES, 0, OFF, FALSE, F, and NO. Default: off.

       --seed-half-exact BOOL
              Allow  errors  only  in  second  half  of seed. One of 1, ON, TRUE, T, YES, 0, OFF,
              FALSE, F, and NO. Default: on.

   Miscellaneous Heuristics:
       --pre-scoring INTEGER
              evaluate score of a region NUM times the size of the seed before extension (0 -> no
              pre-scoring,  1  -> evaluate seed, n-> area around seed, as well; default = 1 if no
              reduction is used). In range [1..10]. Default: 2.

       --pre-scoring-threshold DOUBLE
              minimum average score  per  position  in  pre-scoring  region.  In  range  [0..20].
              Default: 2.

       --filter-putative-duplicates BOOL
              filter  hits  that will likely duplicate a match already found. One of 1, ON, TRUE,
              T, YES, 0, OFF, FALSE, F, and NO. Default: on.

       --filter-putative-abundant BOOL
              If the maximum number of matches per query are found already, stop searching if the
              remaining realm looks unfeasible. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and
              NO. Default: on.

       --merge-putative-siblings BOOL
              Merge seed from one region, stop searching if the remaining realm looks unfeasable.
              One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on.

   Scoring:
       --score-gap INTEGER
              Score per gap character. In range [-1000..1000]. Default: -2.

       --score-gap-open INTEGER
              Additional cost for opening gap. In range [-1000..1000]. Default: -5.

       --score-match INTEGER
              Match score [only BLASTN]) In range [-1000..1000]. Default: 2.

       --score-mismatch INTEGER
              Mismatch score [only BLASTN] In range [-1000..1000]. Default: -3.

   Extension:
       -x, --x-drop INTEGER
              Stop  Banded  extension  if  score x below the maximum seen (-1 means no xdrop). In
              range [-1..1000]. Default: 30.

       -b, --band INTEGER
              Size of the DP-band used in extension (-3 means log2 of query length; -2 means sqrt
              of  query length; -1 means full dp; n means band of size 2n+1) In range [-3..1000].
              Default: -3.

       -m, --extension-mode STRING
              Choice of extension algorithms. One of auto, xdrop, and fullSerial. Default: auto.

TUNING

       Tuning the seeding parameters and (de)activating alphabet reduction has a strong influence
       on both speed and sensitivity. We recommend the following alternative profiles for protein
       searches:

       fast (high similarity):       --seed-delta-increases-length on

       sensitive (lower similarity): --seed-offset 3

       For further information see the wiki: <https://github.com/seqan/lambda/wiki>

LEGAL

       lambda2 searchn 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.