'\" t
.\"     Title: gt-encseq-encode
.\"    Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author]
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 07/22/2020
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.6.1
.\"  Language: English
.\"
.TH "GT\-ENCSEQ\-ENCODE" "1" "07/22/2020" "GenomeTools 1\&.6\&.1" "GenomeTools Manual"
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.SH "NAME"
gt-encseq-encode \- Encode sequence files (FASTA/FASTQ, GenBank, EMBL) efficiently\&.
.SH "SYNOPSIS"
.sp
\fBgt encseq encode\fR sequence_file [sequence_file [sequence_file \&...]]
.SH "DESCRIPTION"
.PP
\fB\-showstats\fR [\fIyes|no\fR]
.RS 4
show compression results (default: no)
.RE
.PP
\fB\-ssp\fR [\fIyes|no\fR]
.RS 4
output sequence separator positions to file (default: yes)
.RE
.PP
\fB\-des\fR [\fIyes|no\fR]
.RS 4
output sequence descriptions to file (default: yes)
.RE
.PP
\fB\-sds\fR [\fIyes|no\fR]
.RS 4
output sequence description separator positions to file (default: yes)
.RE
.PP
\fB\-md5\fR [\fIyes|no\fR]
.RS 4
output MD5 sums to file (default: yes)
.RE
.PP
\fB\-clipdesc\fR [\fIyes|no\fR]
.RS 4
clip descriptions after first whitespace (default: no)
.RE
.PP
\fB\-sat\fR [\fIstring\fR]
.RS 4
specify kind of sequence representation by one of the keywords direct, bytecompress, eqlen, bit, uchar, ushort, uint32 (default: undefined)
.RE
.PP
\fB\-dna\fR [\fIyes|no\fR]
.RS 4
input is DNA sequence (default: no)
.RE
.PP
\fB\-protein\fR [\fIyes|no\fR]
.RS 4
input is protein sequence (default: no)
.RE
.PP
\fB\-plain\fR [\fIyes|no\fR]
.RS 4
process as plain text (default: no)
.RE
.PP
\fB\-indexname\fR [\fIstring\fR]
.RS 4
specify name for index to be generated (default: undefined)
.RE
.PP
\fB\-smap\fR [\fIstring\fR]
.RS 4
specify file containing a symbol mapping (default: undefined)
.RE
.PP
\fB\-lossless\fR [\fIyes|no\fR]
.RS 4
allow lossless original sequence retrieval (default: no)
.RE
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (default: no)
.RE
.PP
\fB\-help\fR
.RS 4
display help for basic options and exit
.RE
.PP
\fB\-help+\fR
.RS 4
display help for all options and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.SH "REPORTING BUGS"
.sp
Report bugs to https://github\&.com/genometools/genometools/issues\&.