---
name: "e-mem"
section: "1"
platform: "linux"
package: "e-mem"
version: "1.0.1-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/e-mem"
---

# e-mem(1)

finds position and length of all Maximal Exact Matches (MEMs) for very large genomes

## NAME

e-mem - finds position and length of all Maximal Exact Matches (MEMs) for very large genomes

## SYNOPSIS

**e-mem** \[*options*\]  *\<reference-file\>  \<query-file\>*

## DESCRIPTION

e-mem finds and outputs the position and length of all maximal exact matches (MEMs) between \<query-file\> and \<reference-file\>

## OPTIONS

- **-n**

  match only the characters a, c, g, or t they can be in upper or in lower case

- **-l**

  set the minimum length of a match. The default length is 50

- **-b**

  compute forward and reverse complement matches

- **-r**

  only compute reverse complement matches

- **-c**

  report the query-position of a reverse complement match relative to the original query sequence

- **-F**

  force 4 column output format regardless of the number of reference sequence input

- **-L**

  show the length of the query sequences on the header line

- **-d**

  set the split size. The default value is 1

- **-t**

  number of threads. The default is 1 thread

- **-h**

  show possible options

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.