Rebuilder

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Rebuilder
Function Assembly
Phase Assembly
Standard CLAs PRE, DATA, RUN, SUBDIR, OUTDIR, GDB, NO_HEADER
Special CLAs min_links, min_insert_size, med_stdev, min_med_stdev_links, high_stdev, min_high_stdev_links, max_stdev, force_min_links, max_overlap_difference, max_overlap_to_accept, max_overlap_score, max_errors_in_align, end_stretch_in_align, kmer_size_in_align, use_sw_gap, affine_in_swgap, max_gap_in_swgap, max_indel_in_swgap, use_specific_pairs, use_specific_pairs_bool, ignore_specific_pairs, use_specific_contigs, use_specific_supers, show_internal_links, check_overlaps, check_coverage, max_coverage_multiple, align_overlaps, keep_existing_supers, rebuild_existing_supers, extend_only, subsume_only, max_merges, min_super_size_to_sanity_check, max_mergeable_super_size, min_mergeable_super_size, min_good_internal_links, use_repetitive_reads, duplicate_template_threshold, stretch_limit, WRITE, LOG_FILE, BRIEF_LOG_FILE, DUPLICATE_TEMPLATE_LOG_FILE, min_read_size, min_spread
Source location ARACHNE_DIR/assemble_alt

The Rebuilder module performs scaffolding; that is, it builds supercontigs out of contigs. It is an important algorithmic step in the assembly process and often causes bottlenecks in runtime and memory usage. It is called "Rebuilder" instead of merely "Builder" because it is often called after a module, such as BreakIt or PositiveBreaker, that breaks apart supercontigs.

Command-line arguments

  • keep_existing_supers (default: False)

If True, instead of breaking up all the existing supers, see if there are any merges that can be made between existing supers.

  • use_repetitive_reads (default: True)

If True, consider links where one or the other read has been flagged by TagRepeatReads.

  • align_overlaps (default: True)

By default, Rebuilder aligns contigs that would overlap, rejects super merges where alignments can't be found for large overlaps. If align_overlaps=False, this check is not performed and the merger is done.

  • extend_only (default: False)

If true, only merges when one super extends another.

  • subsume_only (default: False)

If true, only merges when one super completely subsumes another.

  • use_sw_gap (default: True)

If true, use the Smith-Waterman algorithm to find gap alignments. Note that the default value of this argument was False until February 2008, when it was determined that the Smith-Waterman algorithm was reliably faster.

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