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A tool that postprocesses whole genome alignment (for two or more genomes)and produces coarse-grained synteny blocks. Currently, eitherCactusorSibeliaZ alignments are supported.

This tool is originally a part ofRagout package.

make

Building requires C++11 compiler and development environent installed in your system

    Usage: maf2synteny [-o out_dir] [-s simpl_params] [-m block_sizes] alignment_file       positional arguments:       alignment_filepath to alignment file in maf or gff format        optional arguments:       -o out_dirpath to the output directory [default = .]       -s simpl_paramspath to a file with simplifcation parameters [default = not set]       -b block_sizescomma-separated list of synteny block scales [default = 5000]

maf2synteny takes as input whole genome alignment in.maf or.gff formats.The tool is optimized to work with Cactus or SibeliaZ alignments. Othertools that generate alignments in similar format might not be supported.

The main reason for that is that maf2synteny expect all local alignments to benon-overlapping, which is a very specific kind of whole genome alignmet.Such alignment characterizes all repeated elements in the genome(s)in the alphabet of maximum non-overlapping units. If the input alignmetdoes not have this property, maf2synteny will likely not be able to produce good-qualitysynteny blocks.

One can specify custom graph simplification parameters to controlthe granularity of produced synteny blocks. The paramerscould be supplied in a text file, where each line containstwo numbers:min_block max_gap. Please refer to the paper belowfor the explanation how these parameters control the blockgeneration rpcedure.

Default parameters:{30, 10}, {100, 100}, {500, 1000}, {1000, 5000}, {5000, 15000}

• Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM,Thybert D, Paten B., Pham S. "Chromosome assembly of large and complex genomes using multiple references"Genome research. 2018doi:10.1101/gr.236273.118