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parameter_description.md

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Parameters used by HINGE

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 bacbone assembly, choose the longest n segments for consensus.
  • quality_threshold = 0.23; // alignment quality threshold