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Elmeri is a program to correct errors in raw optical map data (Rmaps).
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README.md

README.md

Elmeri

Elmeri is a program to correct errors in raw optical map data (Rmaps).

Reference

L. Salmela, K. Mukherjee, S.J. Puglisi, M.D. Muggli, and C. Boucher: Fast and accurate correction of optical mapping data with spaced seeds

System Requirements

Elmeri has been tested on systems running Linux on a X86_64 architecture. Elmeri requires that the boost library is available.

Installation

Copy the repository to your own machine and run make in the src directory.

Usage

elmeri [parameters]

Required parameters:
-i input_file Input file of Rmaps to be corrected
-o output_file Output file for corrected Rmaps
Optional parameters:
-l el Size of (el,k)-mers in kbp (default: 80)
-k k Minimum size of (el,k)-mers in number of fragments (default: 5)
-s spacing_pattern Spacing pattern for spaced seeds.(default: 11111111110001110110010010011101001110001010010100001010011000010111100000001100)
-c coverage Maximum number of Rmaps in an alignment. If set to > 64, will be reset to 64. (default: 64)
-t similarity threshold Threshold for merging similar (el,k)-mers in the index. (default: 10)

The default parameters work well on small to medium sized genomes when the coverage of the Rmaps is high. For a large genome such as the human genome, setting k to a higher value (e.g. 6) to ensure that (el,k)-mers are unique in the genome often gives better results. The coverage parameter should be set to reflect the coverage of the Rmap data.

Data format

The input Rmaps should be in the following format. Each Rmap takes three lines in the file. First line gives the name of the Rmap. The second line has two columns for the enzyme and the rest of the columns give the fragment sizes. The third line is empty.

If you have data in the bnx format, the bnx2valouev.py script in the eval folder can be used to convert the data into the correct format:

python bnx2valouev.py input.bnx > input.valouev

Example

An example data set is given in the ecoli-sample folder. This data set is already in the correct format for elmeri. To correct the Rmaps run elmeri as follows:

elmeri -i ecoli-sample/ecoli-2000.valouev -o ecoli-sample/ecoli-2000-corrected.valouev

Outputting Rmaps sharing (el,k)-mers

The elmeri-index binary can be used to output pairs of Rmaps that share (el,k)-mers:

elmeri-index input_Rmaps el output_file spacing_pattern count_threshold merge_similarity_threshold

Parameters:
input_Rmaps Input file of Rmaps to be indexed
el Size of (el,k)-mers in kbp
output_file Output file for pairs of related Rmaps
spacing_pattern Spacing pattern for spaced seeds.(e.g. 11111111110001110110010010011101001110001010010100001010011000010111100000001100)
count_threshold Threshold for the number of shared (el,k)-mers two Rmaps have to share to be considered related.
merge_similarity_threshold Threshold for merging similar (el,k)-mers in the index.

The input Rmaps should be in the same format as for Elmeri. The output is provided in dot graph format where the nodes are the Rmaps (labeled by integers giving their order in the input file) and edges represent relatedness of the Rmaps. The weight of the edges gives the number of (el,k)-mers the Rmaps share.

Changes

17-10-2019: Fixed a bug in merging similar (l,k)-mers. Default merge similarity threshold is now 10 to get similar performance as earlier with default values.

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