---
name: "seqsplit"
section: "1"
platform: "linux"
package: "biosquid"
version: "1.9g+cvs20050121-15.1+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/seqsplit"
---

# seqsplit(1)

split seqs into chunks of defined size and overlap

## NAME

seqsplit - split seqs into chunks of defined size and overlap

## SYNOPSIS

**seqsplit** \[-options\] \<seqfile\>

## DESCRIPTION

This manual page documents briefly the **seqsplit** command.

**seqsplit** is a program that splits sequences into smaller chunks of defined size and overlap; output a FASTA file.

## OPTIONS

- **-h**

  Help; display usage and version.

- **-o \<file\>**

  Output the new FASTA file to \<file\>.

- **--fragfile \<f\>**

  Save one-line-per-frag coord summary file to \<f\>.

- **--informat \<s\>**

  Specify sequence file format \<s\>.

- **--length \<n\>**

  Set max length of each unique seq frag to \<n\>.

- **--overlap \<n\>**

  Set overlap length to \<n\> (total frag size = length+overlap).

- **--shortnames**

  Use short "frag1" names, not "\<src\>/\<from\>-\<to\>".

## LIMITATIONS

Still working in 32 bits -- no sequence can be more than 2 GB in size.

## SEE ALSO

[**afetch**(1)](/afetch/1.md), [**alistat**(1)](/alistat/1.md), [**compalign**(1)](/compalign/1.md), [**compstruct**(1)](/compstruct/1.md), [**revcomp**(1)](/revcomp/1.md), [**seqstat**(1)](/seqstat/1.md), [**sfetch**(1)](/sfetch/1.md), [**shuffle**(1)](/shuffle/1.md), [**sindex**(1)](/sindex/1.md), [**sreformat**(1)](/sreformat/1.md), [**stranslate**(1)](/stranslate/1.md), [**weight**(1)](/weight/1.md).\

## AUTHOR

```
Sean Eddy
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
Phone: 1-314-362-7666
FAX  : 1-314-362-2157
Email: eddy@genetics.wustl.edu
```

This manual page was written by Nelson A. de Oliveira \<naoliv@gmail.com\>, for the Debian project (but may be used by others).