# LAST Performance Tuning

This document tells you how to make LAST faster, at a cost in sensitivity or memory use, or more sensitive, at a cost in speed.

Ideally, the default settings would always work well. Unfortunately, there is too great a variety of challenging alignment tasks, and the LAST developers lack experience with most of them.

LAST must have some defaults, and any choice will displease someone. It is wrong to say "LAST is faster but less sensitive than method X", or "slower but more sensitive than method Y", without varying the defaults.

## lastdb -w

This option reduces memory and disk usage. It makes lastdb and probably lastal faster. By default lastdb indexes every position in the sequence(s), but -w2 makes it index every 2nd position, -w3 every 3rd position, etc. This may reduce sensitivity, but not necessarily, because LAST uses initial matches that are sufficiently rare, and by ignoring some matches the remaining ones become rarer.

Among other aligners, MegaBLAST indexes every 5th position, and BLAT indexes every 11th position.

## lastdb -i

This option makes lastdb faster, but disables some lastal options. If lastdb is too slow, try -i10.

## lastdb -C

This option may make lastal a bit faster, but uses more memory and disk, and makes lastdb slower. If these downsides are no problem, you may as well try it. -C3 is fastest (at least sometimes) but uses most memory, -C2 is almost as fast.

## lastal -m

This option trades speed for sensitivity. It sets the rareness limit for initial matches: initial matches are lengthened until they occur at most this many times in the lastdb volume. The default is 10. So -m100 makes it more sensitive but slower, by using more initial matches.

## lastal -l

This option makes lastal faster but less sensitive. It sets the minimum length of initial matches, e.g. -l50 means length 50. (The default is 1). This can make it much faster, and the sensitivity is adequate if the alignments contain long, gapless, high-identity matches.

## lastal -k

This option makes lastal faster but less sensitive. By default lastal looks for initial matches starting at every position in the query sequence(s), but -k2 makes it check every 2nd position, -k3 every 3rd position, etc. Be careful about combining this with lastdb option -w.

## lastal -x

This option can make lastal faster but less sensitive. It sets the maximum score drop in alignments, in the gapped extension phase. Lower values make it faster, by quitting unpromising extensions sooner. The default aims at best accuracy.

Unfortunately, the default is a complex function of the other parameters and the database size. You can see it in the lastal header after "x=", e.g. by running lastal with no queries. Then try, say, halving it.

## lastal -C

This option (gapless alignment culling) can make lastal faster but less sensitive. It can also reduce redundant output. For example, -C2 makes it discard alignments (before gapped extension) whose query coordinates lie in those of 2 or more stronger alignments.

## lastal -j1

This option requests gapless alignment, which is faster. (You could get the same effect by using very high gap costs, but -j1 is faster because it skips the gapping phase entirely.)

## lastal -f

Option -fTAB reduces the output size, which can improve speed.

## Repeat masking

This can make LAST much faster, produce less output, and reduce memory and disk usage. Please see last-repeats.html.