| layout | page |
|---|---|
| title | Parameters used by HINGE |
All the parameters below can be set using the .ini file read by the HINGE programs.
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length_threshold = 1000;{: style="color: red"} Minimum read length
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aln_threshold = 2500;{: style="color: red"} Minimum alignment length between two reads to be considered when building graph
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min_cov = 5;{: style="color: red"} Minimum coverage depth for a segment on a read to not be considered erroneous/chimeric
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cut_off = 300;{: style="color: red"} 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
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theta = 300;{: style="color: red"} When classifying a match between two reads as a right/left overlap, internal match, etc., overhangs of length up to theta are ignored
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use_qv = true;{: style="color: red"} 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)
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coverage = true;{: style="color: red"} 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.
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coverage_frac_repeat_annotation = 3;{: style="color: red"}
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min_repeat_annotation_threshold = 10;{: style="color: red"}
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max_repeat_annotation_threshold = 20;{: style="color: red"}
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;{: style="color: red"} How far two hinges of the same type can be on a read
- no_hinge_region = 500;{: style="color: red"} Hinges cannot be placed within no_hinge_region of the start and end of the read
- hinge_min_support = 7;{: style="color: red"} Minimum number of reads that have to start in a
reso(default 40) length interval to be considered in hinge calling - hinge_unbridged = 6;{: style="color: red"} Number of reads that one has to see before a pileup to declare a potential hinge unbridged
- hinge_bin = 100;{: style="color: red"} Physical length of the bins considered
- hinge_tolerance_length = 100;{: style="color: red"} Matches starting within hinge_tolerance_length of a hinge are considered to be starting at the hinge
- n_proc = 12;{: style="color: red"} number of CPUs for layout step
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hinge_tolerance = 150;{: style="color: red"} This is how far an overlap must start from a hinge to be considered an internal overlap.
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hinge_slack = 1000;{: style="color: red"} This is the amount by which a forward overlap must be longer than a forward internal overlap to be preferred while building a graph.
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matching_hinge_slack = 200;{: style="color: red"} 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
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min_connected_component_size = 8;{: style="color: red"} 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
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kill_hinge_overlap = 300;{: style="color: red"}
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kill_hinge_internal = 40;{: style="color: red"}
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;{: style="color: red"}
- del_telomeres = 0;{: style="color: red"} 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;{: style="color: red"} If set to 1, the pruning will be more aggressive. We recommend it be set to 1 for large genome.
- use_two_matches = 1;{: style="color: red"} Allow the HINGE algorithm to consider the top two matches between a pair of reads (as opposed to just the longest match)
- tspace = 900;{: style="color: red"} space between new "trace points"
- step = 50;{: style="color: red"}
- min_length = 4000;{: style="color: red"} Minimal length of reads used for final consensus
- trim_end = 200;{: style="color: red"} Trim ends for alignments for final consensus
- best_n = 1;{: style="color: red"} If one read has multiple alignments with the backbone assembly, choose the longest n segments for consensus.
- quality_threshold = 0.23;{: style="color: red"} alignment quality threshold