---
name: "last-split5"
section: "1"
platform: "linux"
package: "last-align"
version: "1447-1+b1"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/last-split5"
---

# last-split5(1)

Estimates "split" or "spliced" alignments.

## NAME

last-split5 - Estimates "split" or "spliced" alignments.

## SYNOPSIS

**last-split5-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