NAME¶

last-split - Estimates "split" or "spliced" alignments.

SYNOPSIS¶

last-split-plain [options] LAST-alignments.maf

DESCRIPTION¶

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.

OPTIONS¶

-h, --help

show this help message and exit

-f, --format=FMT

output format: MAF, MAF+

-r, --reverse

reverse the roles of the 2 sequences in each alignment

-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: 7.0)

-S, --sdev=SDEV

standard deviation of ln[intron length] (default: 1.7)

-m, --mismap=PROB

maximum mismap probability (default: 1.0)

-s, --score=INT

minimum alignment score (default: e OR e+t*ln[100])

-n, --no-split

write original, not split, alignments

-b, --bytes=B

maximum memory (default: 8T for split, 8G for spliced)

-v, --verbose

be verbose

-V, --version

show version information and exit