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 <gt-users@genometools.org>.