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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 https://github.com/genometools/genometools/issues.

01/31/2024 GenomeTools 1.6.5