---
name: "gt-shredder"
section: "1"
platform: "linux"
package: "genometools"
version: "1.6.5+ds-2.2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gt-shredder"
---

# gt-shredder(1)

Shredder sequence file(s) into consecutive pieces of random length.

## NAME

gt-shredder - Shredder sequence file(s) into consecutive pieces of random length.

## SYNOPSIS

**gt shredder** \[option ...\] \[sequence\_file ...\]

## DESCRIPTION

- **-coverage** \[*value*\]

  set the number of times the sequence\_file is shreddered (default: 1)

- **-minlength** \[*value*\]

  set the minimum length of the shreddered fragments (default: 300)

- **-maxlength** \[*value*\]

  set the maximum length of the shreddered fragments (default: 700)

- **-overlap** \[*value*\]

  set the overlap between consecutive pieces (default: 0)

- **-sample** \[*value*\]

  take samples of the generated sequences pieces with the given probability (default: 1.000000)

- **-clipdesc** \[*yes\|no*\]

  clip descriptions after first space (fooled by *\\t*, *\\n* etc) adds offset and length to ensure unique identifier (default: no)

- **-width** \[*value*\]

  set output width for FASTA sequence printing (0 disables formatting) (default: 0)

- **-o** \[*filename*\]

  redirect output to specified file (default: undefined)

- **-gzip** \[*yes\|no*\]

  write gzip compressed output file (default: no)

- **-bzip2** \[*yes\|no*\]

  write bzip2 compressed output file (default: no)

- **-force** \[*yes\|no*\]

  force writing to output file (default: no)

- **-help**

  display help and exit

- **-version**

  display version information and exit

Each sequence given in *sequence\_file* is shreddered into consecutive pieces of random length (between *-minlength* and *-maxlength*) until it is consumed. By this means the last shreddered fragment of a given sequence can be shorter than the argument to option *-minlength*. To get rid of such fragments use gt seqfilter (see example below).

## EXAMPLES:

Shredder a given BAC:

```
$ gt shredder U89959_genomic.fas > fragments.fas
```

Shredder an EST collection into pieces between 50 and 100 bp and get rid of all (terminal) fragments shorter than 50 bp:

```
$ gt shredder -minlength 50 -maxlength 100 U89959_ests.fas \
  | gt seqfilter -minlength 50 - > fragments.fas
# 130 out of 1260 sequences have been removed (10.317%)
```

Shredder an EST collection and show only random 10% of the resulting fragments:

```
$ gt shredder -sample 0.1 U89959_ests.fas
```

## REPORTING BUGS

Report bugs to https://github.com/genometools/genometools/issues.