synolog_linkint.py
The synolog_linkint.py script reads the 'annotation_integration.map' file in the species cache and sets a series of symbolic links to connect the specific genome annotations to their respective genome integrations (e.g. a scaffold-level assembly integrated with Hi-C data or a contig-level assemblywith a genetic map). A single scaffold-level annotation (and its resulting BLAST hits) can be used with several alternative genome integrations, where the gene positions have been translated to the integrated assembly.
Other Pipeline Programs
Core
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Species Cache
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Execution control
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Utility programs
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The synolog program assigns orthologs and identifies regions of conserved synteny.
The synolog_cctl.py program adds, updates, or removes genome data from the species data cache.
The synolog_blast.py creates and queues BLAST jobs between species annotations on a SLURM scheduler.
The synolog_ncgenes.py allows for the import of non-coding genes into the species cache.
The synolog_link.py program links BLAST results for species annotations to a particular species assembly.
The synolog_run.py program executes Synolog on a particular subset of species from the stored data cache.
The synolog_fasta.py program exports ortholog data in FASTA format for different downstream analyses.
The synolog_info.py program displays information for particular orthogroups from the data cache and Synolog run.
The synolog_plot.py program plots conserved synteny between species.
The synolog_collinearize.py program scaffolds a genome together based on shared synteny.
