lastdb
======

This program prepares sequences for subsequent comparison and
alignment using lastal.  You can use it like this:

  lastdb humanDb humanChromosome*.fasta

This will read files called humanChromosome*.fasta, and write several
files whose names begin with humanDb.

Input
-----

The input should be one or more files in fasta format, which looks
like this:

  >MyFirstSequence
  ATCGGGATATATGGAGAGCTTAGAG
  TTTGGATATG
  >My2ndSequence
  TTTAGAGGGTTCTTCGGGATT

If you wish to read standard input (e.g. from a pipe), use the special
file name "-".

Options
-------

Main Options
~~~~~~~~~~~~

  -h  Show all options and their default settings.

  -p  Interpret the sequences as proteins.  The default is to interpret
      them as DNA.

  -c  Soft-mask lowercase letters.  This means that, when we compare
      these sequences to some other sequences using lastal, lowercase
      letters will be excluded from initial matches.  This will apply
      to lowercase letters in both sets of sequences.

Advanced Options
~~~~~~~~~~~~~~~~

  -Q NUMBER
      Specify the input format.  0 means fasta, 1 means fastq-sanger,
      2 means fastq-solexa, and 3 means fastq-illumina.  The fastq
      formats provide sequence quality data, which will be stored by
      lastdb and then used by lastal.  These formats are described in
      lastal.txt.

  -w STEP
      Allow initial matches to start only at every STEP-th position in
      each of the sequences given to lastdb.  This reduces the memory
      usage of lastdb and lastal, and it makes lastdb faster.  Its
      effect on the speed and sensitivity of lastal is not entirely
      clear.  To emulate BLAT, use "-w 11".

  -s BYTES      
      Limit memory usage, by splitting the output files into smaller
      "volumes" if necessary.  This will limit the memory usage of
      both lastdb and lastal, but it will make lastal slower.  It is
      also likely to change the exact results found by lastal.

      Each volume will have at most BYTES bytes.  (Roughly.  The more
      masked letters or DNA "N"s, the more it will undershoot.)  You
      can use suffixes K, M, and G to specify KibiBytes, MebiBytes,
      and GibiBytes (e.g. "-s 5G").

      However, the output for one sequence is never split.  Since the
      output files are several-fold bigger than the input (unless you
      use -w), this means that mammalian chromosomes cannot be
      processed using much less than 2G (unless you use -w).

      There is a hard upper limit of about 4 billion sequence letters
      per volume.  Together with the previous point, this means that
      lastdb will refuse to process any single sequence longer than
      about 4 billion.

  -m PATTERN
      Specify a spaced seed pattern, for example "-m 110101".  In this
      example, mismatches will be allowed at every third and fifth
      position out of six in initial matches.

      This option does not constrain the length of initial matches.
      The pattern will get cyclically repeated as often as necessary
      to cover any length.

      Although the 0 positions allow mismatches, they exclude
      non-standard letters (e.g. non-ACGT for DNA).  If option -c is
      used, they also exclude lowercase letters.

      You can also specify transition constraints, e.g "-m 100TT1".
      In this example, transitions (but not transversions) will be
      allowed at every fourth and fifth position out of six.
      Alternatively, you can use Iedera's notation, for example
      "-m '#@#--##--#-#'" ('#' for match, '@' for transition, '-' or
      '_' for mismatch).

      You can specify multiple patterns by separating them with commas
      and/or using "-m" multiple times.

  -u FILE
      Specify a subset seed file. For an example of the format, see
      yass.seed in the examples directory.  You can specify multiple
      files by using "-u" multiple times.

  -a SYMBOLS
      Specify your own alphabet, e.g. "-a 0123".  The default (DNA)
      alphabet is equivalent to "-a ACGT".  The protein alphabet (-p)
      is equivalent to "-a ACDEFGHIKLMNPQRSTVWY".  Non-alphabet
      letters are allowed in sequences, but by default they are
      excluded from initial matches and get the mismatch score when
      aligned to anything.  If -a is specified, -p is ignored.

  -i MATCHES
      This option makes lastdb faster, at the expense of limiting your
      options with lastal.  If you use (say) "-i 10", then you cannot
      use lastal with option m < 10.

  -b DEPTH
      Specify the depth of "buckets" used to accelerate initial match
      finding.  Larger values increase the memory usage of lastdb and
      lastal, make lastal faster, and have no effect on lastal's
      results.  The default is to use the maximum depth that consumes
      at most one byte per possible match start position.

  -x  Just count sequences and letters.  This is much faster, and the
      results are useful with lastex.  Letter counting is never
      case-sensitive.

  -v  Be verbose: write messages about what lastdb is doing.

Limitations
-----------

lastdb can become catastrophically slow for highly redundant
sequences, e.g. two almost-identical genomes.  It usually processes
several GB per hour, but if it becomes much slower, try option "-i
10", which is likely to solve the problem.  (If even that is too slow,
try "-i 100" or so.)
