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.