last-split(1) Estimates split or spliced alignments.


last-split [,options/] ,LAST-alignments.maf/


Read alignments of query sequences to a genome, and estimate the genomic source of each part of each query, allowing different parts of one query to come from different parts of the genome.


-h, --help
show this help message and exit
-g, --genome=,NAME/
lastdb genome name
-d, --direction=,D/
RNA direction: 0=reverse, 1=forward, 2=mixed (default=1)
-c, --cis=,PROB/
cis-splice probability per base (default=0.004)
-t, --trans=,PROB/
trans-splice probability per base (default=1e-05)
-M, --mean=,MEAN/
mean of ln[intron length] (default=7)
-S, --sdev=,SDEV/
standard deviation of ln[intron length] (default=1.7)
-m, --mismap=,PROB/
maximum mismap probability (default=0.01)
-s, --score=,INT/
minimum alignment score (default=e OR e+t*ln[1000])
-n, --no-split
write original, not split, alignments
-v, --verbose
be verbose
-V, --version
show version information and exit