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LAST-SPLIT8(1) User Commands LAST-SPLIT8(1)

NAME

last-split8 - Estimates "split" or "spliced" alignments.

SYNOPSIS

last-split8-avx2 [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

show this help message and exit
output format: MAF, MAF+ (default=MAF+)
lastdb genome name
RNA direction: 0=reverse, 1=forward, 2=mixed (default=1)
cis-splice probability per base (default=0.004)
trans-splice probability per base (default=1e-05)
mean of ln[intron length] (default=7)
standard deviation of ln[intron length] (default=1.7)
maximum mismap probability (default=1)
minimum alignment score (default=e OR e+t*ln[100])
write original, not split, alignments
maximum memory (default=8T for split, 8G for spliced)
be verbose
show version information and exit
March 2021 last-split8 1179