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gt-readjoiner-prefilter(1)


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>.



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