GenomeTools - manual page for GT-ENCSEQ-ENCODE(1)

## 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.