#29 · Tools & infrastructure

Integrated pipelines and platforms are consolidating multi-step genomic analyses

The common thread is consolidation of multi-step genomic analysis into end-to-end, automated or interactive environments. SLCNV chains QC, CNV calling, segmentation, plotting and clustering for low-pass whole-genome sequencing in a containerized Nextflow/Docker pipeline. BUDDY combines alignments, structure viewing, pathogenicity predictions and CRISPR reagent design in a web platform for modeling human missense variants through S. cerevisiae orthologs. mobileRNA applies automated multi-genome alignment to identify mobile RNAs in grafted plants, validated on simulated grafts. Vizitig shifts the unit of analysis to colored de Bruijn graphs, enabling interactive querying across samples for pangenome and pantranscriptome work. What is new here is the integration layer itself: packaged workflows for sequencing-derived copy number analysis, cross-tool assembly of alignment, structure and reagent design for variant functional modeling, and graph-based cross-sample exploration.