Scroll to navigation

LAST-SPLIT(1) User Commands LAST-SPLIT(1)

NAME

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

SYNOPSIS

last-split-avx [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+ (default=MAF+)
-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=1)
-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
December 2020 last-split 1169