Methods and systems for large scale scaffolding of genome assemblies

A system for performing large scale scaffolding of a genome assembly comprising:

• a computer readable storage medium which stores computer-executable instructions comprising
• instructions for applying a location clustering model to a test set of contigs to form two or more location cluster groups, each location cluster group comprising one or more location-clustered contigs;
• instructions for applying an ordering model to each of the two or more location cluster groups to form an ordered set of one or more location-clustered contigs within each cluster group;
• and
• instructions for applying an orienting model to each ordered set of one or more location-clustered contigs to assign a relative orientation to each of the location-clustered contigs within each location cluster group;
• wherein the test set of contigs are generated from aligning a set of reads generated by a chromosome conformation analysis technique with a draft assembly, a reference assembly, or both.
• a processor which is configured to perform steps comprising
• receiving a set of input files which comprise
• a file comprising the set of reads generated by a chromosome conformation analysis technique;
• and
• the draft assembly, reference assembly, or both;
• executing the computer-executable instructions stored in the computer-readable storage medium.

A computer readable storage medium which stores computer-executable instructions comprising:

• instructions for applying a location clustering model to a test set of contigs to form two or more location cluster groups, each location cluster group comprising one or more location-clustered contigs;
• instructions for applying an ordering model to each of the two or more location cluster groups to form an ordered set of one or more location-clustered contigs within each cluster group;
• instructions for applying an orienting model to each ordered set of one or more location-clustered contigs to assign a relative orientation to each of the location-clustered contigs within each location cluster group;
• and
• instructions for applying a species clustering model to a heterogeneous set of contigs to form two or more species cluster groups, each species cluster group comprising one or more species-clustered contigs from a single species;
• wherein the test set of contigs are generated from aligning a set of reads generated by a chromosome conformation analysis technique with a draft assembly, a reference assembly, or both;
• wherein the heterogeneous set of contigs are generated from aligning a set of reads generated by a chromosome conformation analysis technique with a metagenome assembly, and
• wherein the one or more species-clustered contigs are used as the test set of contigs in the instructions for applying a location clustering model.