---
name: "seqcons"
section: "1"
platform: "linux"
package: "seqan-apps"
version: "1.3.1-1"
release: "Debian 7 (Wheezy)"
platforms: ["linux"]
url: "https://new.carta.tech/seqcons"
---

# seqcons(1)

Multi-read alignment

## NAME

seqcons - Multi-read alignment

## SYNOPSIS

**seqcons** *-r \<FASTA file with reads\>* \[*Options*\]

## DESCRIPTION

Multi-read alignment - SeqCons

-

  seqcons **-a** \<AMOS message file\> \[Options\]

- **-h**, **--help**

  displays this help message

- **-V**, **--version**

  print version information

### Main Options:

- **-r**, **--reads** \<FASTA reads file\>

  file with reads

- **-a**, **--afg** \<AMOS afg file\>

  message file

- **-o**, **--outfile** \<Filename\>

  output filename (default align.txt)

- **-f**, **--format** \[seqan \| afg\]

  output format (default afg)

- **-m**, **--method** \[realign \| msa\]

  alignment method (default realign)

- **-b**, **--bandwidth** \<Int\>

  bandwidth (default 8)

- **-n**, **--noalign**

  no align, only convert input

### MSA Method Options:

- **-ma**, **--matchlength** \<Int\>

  min. overlap length (default 15)

- **-qu**, **--quality** \<Int\>

  min. overlap precent identity (default 80)

- **-ov**, **--overlaps** \<Int\>

  min. number of overlaps per read (default 3)

- **-wi**, **--window** \<Int\>

  window size (default 0) /\*If this parameter is \> 0 then all

-

  overlaps within a given window are computed.\*/

### ReAlign Method Options:

- **-in**, **--include**

  include contig sequence

- **-rm**, **--rmethod** \[nw \| gotoh\]

  realign method (default gotoh)

## AUTHOR

seqcons was written by Tobias Rausch

This manual page was generated using html2man and polished by Soeren Sonnenburg \<sonne@debian.org\>, for the Debian project (but may be used by others).