Includes QC, trimming, assembly (hybrid or short reads), variant calling, annotation, and genome reports.
From alignment and transcript quantification to differential expression and pathway analysis (DESeq2, EdgeR).
Microbiome profiling using QIIME2, HUMAnN, MetaPhlAn, R; diversity metrics, taxonomy, functional prediction.
ONT + Illumina integration via Flye, Medaka, Pilon for accurate long-read genome assembly etc.
AMR gene profiling (CARD, ResFinder), virulence prediction, and MLST/serotype analysis.
Publication-ready figures: heatmaps, volcano plots, Circos plots, PCA, phylogenetic trees, KEGG pathways.