---
name: "DistanceEst"
section: "1"
platform: "linux"
package: "abyss"
version: "2.3.10-1+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/DistanceEst"
---

# DistanceEst(1)

Estimate distances between contigs using paired-end alignments.

## NAME

DistanceEst - Estimate distances between contigs using paired-end alignments.

## SYNOPSIS

**DistanceEst** *-k\<kmer\> -s\<seed-length\> -n\<npairs\>* \[*OPTION*\]... *HIST* \[*PAIR*\]

## DESCRIPTION

Estimate distances between contigs using paired-end alignments.

-

  Arguments:

- HIST

  distribution of fragments size

- PAIR

  alignments between contigs

-

  Options:

- **--mind**=*N*

  minimum distance between contigs \[-(k-1)\]

- **--maxd**=*N*

  maximum distance between contigs

- **--fr**

  force the orientation to forward-reverse

- **--rf**

  force the orientation to reverse-forward

- **-k**, **--kmer**=*N*

  set **--mind** to -(k-1) bp

- **-l**, **--min-align**=*N*

  the minimal alignment size \[1\]

- **-n**, **--npairs**=*NPAIRS*

  minimum number of pairs

- **-s**, **--seed-length**=*L*

  minimum length of the seed contigs

- **-q**, **--min-mapq**=*N*

  ignore alignments with mapping quality less than this threshold \[10\]

- **-o**, **--out**=*FILE*

  write result to FILE

- **--mle**

  use the MLE \[default\] (maximum likelihood estimator)

- **--median**

  use the difference of the population median and the sample median

- **--mean**

  use the difference of the population mean and the sample mean

- **--dist**

  output the graph in dist format \[default\]

- **--dot**

  output the graph in GraphViz format

- **--gv**

  output the graph in GraphViz format

- **--gfa**

  output the graph in GFA2 format

- **--gfa2**

  output the graph in GFA2 format

- **-j**, **--threads**=*N*

  use N parallel threads \[1\]

- **-v**, **--verbose**

  display verbose output

- **--help**

  display this help and exit

- **--version**

  output version information and exit

- **--db**=*FILE*

  specify path of database repository in FILE

- **--library**=*NAME*

  specify library NAME for sqlite

- **--strain**=*NAME*

  specify strain NAME for sqlite

- **--species**=*NAME*

  specify species NAME for sqlite

## AUTHOR

Written by Jared Simpson and Shaun Jackman.

## REPORTING BUGS

Report bugs to \<abyss-users@bcgsc.ca\>.

## COPYRIGHT

Copyright 2014 Canada's Michael Smith Genome Sciences Centre