NAME
gt-readjoiner-prefilter - Remove contained and low-quality reads and encode read set in GtEncseq format.
SYNOPSIS
gt readjoiner prefilter [option …]
DESCRIPTION
- -readset [string]
- 
specify the readset name default: filename of first input sequence_file 
- -db
- 
specify a list of input libraries (Fasta/FastQ); for single-end libraries use the filename (which is not allowed to contain : symbols); for paired-end libraries with reads interleaved (f,r,f,r,…) in a single file use the notation <filename>:<insertlength>[,<stdev>] (stdev may be omitted); for paired-end with reads in two files (f, r) use the notation <file_f>:<file_r>:<insertlength>[,<stdev>] 
- -v [yes|no]
- 
be verbose (default: no) 
- -q [yes|no]
- 
suppress standard output messages (default: no) 
- -des [yes|no]
- 
store Fasta IDs (or entire descriptionsif used together with -clipdes no) warning: increases the memory requirement (default: no) 
- -clipdes [yes|no]
- 
clip Fasta descriptions after first space set to false if you need entire descriptions (default: yes) 
- -memdes [yes|no]
- 
use memory storage for descriptions (default: use temporary disk storage) 
- -maxlow [value]
- 
maximal number of low-quality positions in a read default: infinite 
- -lowqual [value]
- 
maximal quality for a position to be considered low-quality (default: 3) 
- -phred64 [yes|no]
- 
use phred64 scores for FastQ format (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.