RecycleGarbage

From ArachneWiki

RecycleGarbage is a tool to clean, edit or modify assemblies by deleting certain types of contigs and supercontigs.

Contents 1 Types of contigs deleted 1.1 Contigs dumped under the default settings 1.2 Contigs not dumped under the default settings 2 Arguments

Types of contigs deleted

Contigs dumped under the default settings

• Bad contigs: Contigs at the ends of scaffolds that do not have a single internal, consistent read pair. Controlled by DUMP_BAD, which in turn is controlled by the Assemblez parameter recycle_bad_contigs.
• Stupid contigs: Small contigs inside scaffolds that have negative gaps on both sides. These contigs are often in the way of merging contigs.
• Contained contigs: Contigs that are entirely subsumed within another contig.

Contigs not dumped under the default settings

• Singletons: Contigs that contain only one or fewer reads.

Arguments

All reads, contigs, and supercontigs are referred to by id unless otherwise specified.

Argument name	Argument type	Default value	Meaning
CONTIGS_TO_DUMP	Index list	[None]	Dump these contigs.
CONTIGS_TO_KEEP	Index list	[None]	Dump all contigs except these.
SUPERS_TO_DUMP	Index list	[None]	Dump these supers.
SUPERS_TO_KEEP	Index list	[None]	Dump all supers except these.
READS_TO_DUMP	Index list	[None]	Dump these reads. Contigs are not broken in bald spots.
READ_NAMES_TO_DUMP	Filename	[None]	Dump the reads in this file. The file format is like reads.to_exclude.
READS_TO_DUMP_FILE	Filename	[None]	Dump the reads in this file. The file format is like reads.to_exclude, but with read ids instead of names.
CONTIGS_TO_DUMP_READS	Index list	[None]	Restricts READS_TO_DUMP, READ_NAMES_TO_DUMP or READS_TO_DUMP_FILE to dump only reads in the contigs listed here.
DUMP_BAD	Bool	True	Dumps bad reads. Also dump small single-contig scaffolds without internal linking.
DUMP_STUPID	Bool	True	Dumps stupid reads.
REMOVE_CONTAINED	Bool	True	Dumps contained reads.
REMOVE_SINGLETONS	Bool	False	Dumps singleton contigs.
REMOVE_LOPSIDED	Bool	False	This is stub code. Leave at default.
LOPSIDE_LAP	Integer	100	This is stub code. Leave at default.
SUPERS_TO_DESINTEGRATE	Index list	[None]	Destroy the supercontig structure in these scaffolds.
CONTIGS_TO_BREAK_SUPERS	Index list	[None]	Break scaffolds right before these contigs.
DUMP_SUPER_ENDS	Bool	True	If False, do not dump bad contigs at the ends of scaffolds, and only dump single-contig scaffolds if there is no internal linking.