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.

GenomeTools 1.6.5                                  04/27/2024                                GT-ENCSEQ-ENCODE(1)