---
name: "gt-encseq-encode"
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-encseq-encode"
---

# gt-encseq-encode(1)

Encode sequence files (FASTA/FASTQ, GenBank, EMBL) efficiently.

## NAME

gt-encseq-encode - Encode sequence files (FASTA/FASTQ, GenBank, EMBL) efficiently.

## SYNOPSIS

**gt encseq encode** sequence\_file \[sequence\_file \[sequence\_file ...\]\]

## DESCRIPTION

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

  show compression results (default: no)

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

  output sequence separator positions to file (default: yes)

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

  output sequence descriptions to file (default: yes)

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

  output sequence description separator positions to file (default: yes)

- **-md5** \[*yes\|no*\]

  output MD5 sums to file (default: yes)

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

  clip descriptions after first whitespace (default: no)

- **-sat** \[*string*\]

  specify kind of sequence representation by one of the keywords direct, bytecompress, eqlen, bit, uchar, ushort, uint32 (default: undefined)

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

  input is DNA sequence (default: no)

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

  input is protein sequence (default: no)

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

  process as plain text (default: no)

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

  mask low-complexity regions using the dust algorithm (default: no)

- **-dustwindow** \[*value*\]

  windowsize for the dust algorithm (default: 64)

- **-dustthreshold** \[*value*\]

  threshold for the dust algorithm (default: 2.000000)

- **-dustlink** \[*value*\]

  Max. distance between regions masked by dust before merging. (default: 1)

- **-indexname** \[*string*\]

  specify name for index to be generated (default: undefined)

- **-smap** \[*string*\]

  specify file containing a symbol mapping (default: undefined)

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

  allow lossless original sequence retrieval (default: no)

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

  be verbose (default: no)

- **-help**

  display help for basic options and exit

- **-help+**

  display help for all options and exit

- **-version**

  display version information and exit

## REPORTING BUGS

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