DOKK / manpages / debian 11 / coop-computing-tools / sand_compress_reads.1.en
sand_compress_reads(1) Cooperative Computing Tools sand_compress_reads(1)

sand_compress_reads - compress sequence data

sand_compress_reads [-qcivh] [infile] [outfile]

sand_compress_reads reads sequence data in standard FASTA format, and produces output in the compressed FASTA (cfa) format used by the sand_filter_master(1) and sand_align_master(1).

If the output file is omitted, standard output is used. if the input file is omitted, standard input is used. After completing the compression, this program will output a summary line of sequences and bytes compressed.

 -q
Quiet mode: suppress summary line.
 -c
Remove Celera read ids if data came from the Celera gatekeeper.
 -i
Remove Celera read ids but leave internal ids if the data came from the Celera gatekeeper.
 -h
Display version information.
 -v
Show help text.

On success, returns zero. On failure, returns non-zero.

To compress mydata.fasta into mydata.cfa:

% sand_compress_reads mydata.fasta mydata.cfa

The Cooperative Computing Tools are Copyright (C) 2005-2019 The University of Notre Dame. This software is distributed under the GNU General Public License. See the file COPYING for details.

CCTools 7.1.2 FINAL