Some next generation sequencing (NGS) analyses are “frequently requested”, for these established and commonly utilized software are utilized (for example, see Table below). Some requests are “routinely-unique”, for these we also use, open source software which are peer-reviewed and published in PubMed; when there is a need to develop new workflows, the R+D is performed and new workflows are developed and utilized (for example, NET-seq, RIBO-seq). Many of the workflows utilize snakemake/nextflow frameworks. All datasets for the projects undergo quality control assessments.
Table below shows some frequently requested NGS analyses.
| Workflows | Outcomes | Software |
| mRNA-seq, microRNA-seq | QC, gene expression, gene differential expression | STAR, HTSeq-count, DEseq2 |
| Single-cell RNA-seq | QC, identify highly variable genes, marker identification, cluster annotation, trajectory inference, composition analysis, differential analysis | STAR, Cell Ranger, Loupe Browser, Seurat |
| Exome-seq, Genome-seq, Targeted re-sequencing | QC, germline mutation profiling, somatic mutational profiling | BWA mem, GATK4 (germline), GATK4 Mutect2 (somatic) |
| ChIP-seq | QC, chIP-seq peak-calling and differential analysis | Bowtie2, MACS2, HOMER, deepTools, ChIPpeakAnno |
| ATAC-seq | QC, ATAC-seq peak-calling and differential analysis | Bowtie2, MACS2, HOMER, deepTools |
| Methyl-seq | QC, bisulfite-sequencing to characterize the methylome (hyper methylated or hypo-methylated regions of the genome) | Bowtie2, Bismark, Metilene |
