gt-readjoiner-prefilter1
Remove contained and low-quality reads and encode read set in gtencseq format.
Usage
gt readjoiner
prefilter
[option ...]
Overview
-
-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
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.