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gt-readjoiner-prefilter - Remove contained and low-quality reads and encode read set in GtEncseq format.


gt readjoiner prefilter [option ...]


-readset [string]

specify the readset name default: filename of first input sequence_file


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)


display help for basic options and exit


display help for all options and exit


display version information and exit


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04/27/2024 GenomeTools 1.6.5