Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes. For this, it uses the genomic structural annotations between multiple chromosome-level assemblies. The genome-wide alignments are performed with Minimap2.

References:

Goel M, Schneeberger K. 2022. plotsr: visualizing structural similarities and rearrangements between multiple genomes. Bioinformatics. 2022 May 13;38(10):2922-2926. doi: 10.1093/bioinformatics/btac196. PMID: 35561173; PMCID: PMC9113368.

Goel M, Sun H, Jiao WB, Schneeberger K. 2019. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 2019 Dec 16;20(1):277. doi: 10.1186/s13059-019-1911-0. PMID: 31842948; PMCID: PMC6913012.

Li H. 2021. New strategies to improve minimap2 alignment accuracy, Bioinformatics, Volume 37, Issue 23, December 2021, Pages 4572–4574, doi: 10.1093/bioinformatics/btab705

Versions: {% if 'PLOTSR' in all_stats_dicts['VERSIONS'] %}{{ all_stats_dicts['VERSIONS']['PLOTSR']['plotsr'] }} (PLOTSR), {% endif %}{{ all_stats_dicts['VERSIONS']['SYRI']['syri'] }} (SYRI), {{ all_stats_dicts['VERSIONS']['MINIMAP2_ALIGN']['minimap2'] }} (MINIMAP2)

{% include 'synteny_plotsr/report_contents.html' %}