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GT-READJOINER-ASSE(1) GenomeTools Manual GT-READJOINER-ASSE(1)

NAME

gt-readjoiner-assembly - Construct string graph and output contigs.

SYNOPSIS

gt readjoiner assembly [option ...]

DESCRIPTION

-readset [string]
specify the readset name (default: undefined)
-spmfiles [value]
number of SPM files to read this must be equal to the value of -j for the overlap phase (default: 1)
-l [value]
specify the minimum SPM length (default: 0)
-depthcutoff [value]
specify the minimal number of nodes in a contig (default: 3)
-lengthcutoff [value]
specify the minimal length of a contig (default: 100)
-errors [yes|no]
search graph features which may originate from sequencing errors and remove them (default: no)
-bubble [value]
number of rounds of p-bubble removal to perform (default: 3)
-deadend [value]
number of rounds of dead end removal to perform a dead end (default: 10)
-deadend-depth [value]
specify the maximal depth of a path to an end-vertex by which the path shall be considered a dead end (default: 10)
-v [yes|no]
be verbose (default: no)
-q [yes|no]
suppress standard output messages (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>.
07/29/2016 GenomeTools 1.5.9