RecycleGarbage

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

Contents

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.
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