Parameters used by HINGE

• 
  fx
• 
  gmk
• 
  is

All the parameters below can be set using the .ini file read by the HINGE programs.

Filter

• length_threshold = 1000; Minimum read length
• aln_threshold = 2500; Minimum alignment length between two reads to be considered when building graph
• min_cov = 5; Minimum coverage depth for a segment on a read to not be considered erroneous/chimeric
• cut_off = 300; When looking for chimeric segments, we look for coverage gaps on a read, after reducing all matches by cut_off in the beginning and in the end
• theta = 300; When classifying a match between two reads as a right/left overlap, internal match, etc., overhangs of length up to theta are ignored
• use_qv = true; Use qv scores provided by DAligner when creating the read masks (i.e., the part of the read that will actually be used for assembly)
• coverage = true; Use coverage values when creating the read masks. If both use_qv and coverage are set to true, an intersection of the two masks is taken.
• coverage_frac_repeat_annotation = 3;
• min_repeat_annotation_threshold = 10;

• max_repeat_annotation_threshold = 20;

  A repeat annotation is placed on the read at position i+reso if

 |coverage[i]-coverage[i+reso]| > min( max( coverage[i+reso]/coverage_frac_repeat_annotation, min_repeat_annotation_threshold), max_repeat_annotation_threshold)

• repeat_annotation_gap_threshold = 300; How far two hinges of the same type can be on a read
• no_hinge_region = 500; Hinges cannot be placed within no_hinge_region of the start and end of the read
• hinge_min_support = 7; Minimum number of reads that have to start in a reso (default 40) length interval to be considered in hinge calling
• hinge_unbridged = 6; Number of reads that one has to see before a pileup to declare a potential hinge unbridged
• hinge_bin = 100; Physical length of the bins considered
• hinge_tolerance_length = 100; Matches starting within hinge_tolerance_length of a hinge are considered to be starting at the hinge

Running

• n_proc = 12; number of CPUs for layout step

Layout

• hinge_tolerance = 150; This is how far an overlap must start from a hinge to be considered an internal overlap.

• hinge_slack = 1000; This is the amount by which a forward overlap must be longer than a forward internal overlap to be preferred while building a graph.

• matching_hinge_slack = 200; We identify two in-hinges (out-hinges) on two different reads as corresponding to the same repeat event, if the reads match in the repeat part, and the two hinges are within matching_hinge_slack of each other
• min_connected_component_size = 8; In order to actually add a hinge to a read, we require that at least min_connected_component_size reads have a repeat annotation and they are all identified as the beginning (or end) of the same repeat
• kill_hinge_overlap = 300;

• kill_hinge_internal = 40;

  When filtering hinges (so that only one in-hinge and one out-hinge are left for each reapeat), we kill an in-hinge (out-hinge) if there is a forward (backward) extension read that starts at least kill_hinge_overlap before (after) the hinge, or if there is a forward_internal (backward_internal) extension read that starts at most kill_hinge_internal after (before) the hinge, as illustrated below.

• num_events_telomere = 7;
• del_telomeres = 0; If set to 1, any read with more than num_events_telomere repeat annotations will be classified as a telomere read and will be deleted.
• aggressive_pruning = 0; If set to 1, the pruning will be more aggressive. We recommend it be set to 1 for large genome.
• use_two_matches = 1; Allow the HINGE algorithm to consider the top two matches between a pair of reads (as opposed to just the longest match)

Draft

• tspace = 900; space between new “trace points”
• step = 50;

Consensus

• min_length = 4000; Minimal length of reads used for final consensus
• trim_end = 200; Trim ends for alignments for final consensus
• best_n = 1; If one read has multiple alignments with the backbone assembly, choose the longest n segments for consensus.
• quality_threshold = 0.23; alignment quality threshold