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