This is the command gt-readjoiner-prefilter that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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>.
Use gt-readjoiner-prefilter online using onworks.net services
