-w STEP |
Allow initial matches to start only at every STEP-th position in
each of the sequences given to lastdb (positions 0, STEP,
2×STEP, etc). 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. |
-W SIZE |
Allow initial matches to start only at positions that are
"minimum" in any window of SIZE consecutive positions.
"Minimum" means that the sequence starting here is
alphabetically earliest.
The "alphabetical" order depends on the seed pattern. The letter order is determined by the
order of the letter groups, and letters in the same group are
considered equivalent.
The fraction of positions that are "minimum" is roughly: 2 /
(SIZE + 1).
|
-S STRAND |
Specify which strand of the input sequences should be prepared
for alignment: 0 means reverse only, 1 means forward only, and 2
means both. |
-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 or -W), this means that mammalian chromosomes cannot be
processed using much less than 2G (unless you use -w or -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.
|
-Q NUMBER |
Specify how to read the sequences. The default is fasta, 0
means fasta or fastq-ignore, 1 means fastq-sanger, 2 means
fastq-solexa, and 3 means fastq-illumina. The fastq formats are
described in lastal.html. |
-P THREADS |
Divide the work between this number of threads running in
parallel. 0 means use as many threads as your computer claims
it can handle simultaneously. |
-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.
|
-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. As a special case, for the DNA alphabet,
Us are converted to Ts. 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. |
-C NUMBER |
Specify the type of "child table" to make: 0 means none, 1 means
byte-size (uses a little more memory), 2 means short-size (uses
somewhat more memory), 3 means full (uses a lot more memory).
Choices > 0 make lastal a bit faster, but make lastdb slower,
and have no effect on lastal's results. Some tests suggest that
-C2 is a good choice: faster than -C1 and no slower than -C3. |
-x |
Just count sequences and letters. This is much faster. Letter
counting is never case-sensitive. |
-v |
Be verbose: write messages about what lastdb is doing. |
-V, --version |
Show version information, and exit. |