specify the readset name default: filename of first input sequence_file (default: undefined)

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>]

be verbose (default: no)

suppress standard output messages (default: no)

store Fasta IDs (or entire descriptionsif used together with -clipdes no) warning: increases the memory requirement (default: no)

clip Fasta descriptions after first space set to false if you need entire descriptions (default: yes)

use memory storage for descriptions (default: use temporary disk storage) (default: no)

maximal number of low-quality positions in a read default: infinite (default: undefined)

maximal quality for a position to be considered low-quality (default: 3)

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