DESeq2 is one of the most widely used tools for differential gene expression analysis in RNA-seq experiments. It is powerful, well documented, and suitable for many standard bulk RNA-seq designs. However, it is also easy…
If you have assembled a bacterial or archaeal genome, the next question is usually straightforward: which annotation pipeline should you use? Three of the most widely used options are Prokka, NCBI PGAP, and RAST. All…
Introduction Shotgun metagenomics allows researchers to sequence all genetic material in an environmental sample. However, after assembly, the resulting dataset contains thousands of contigs from multiple organisms. To reconstruct individual microbial genomes, these contigs must…
Learn how to assemble a bacterial genome from Oxford Nanopore sequencing reads. This guide explains the complete genome assembly workflow using long-read sequencing data.
Introduction Metagenomics has transformed the study of microbial communities by enabling researchers to analyze DNA directly from environmental samples. Instead of isolating organisms in culture, sequencing environmental DNA allows scientists to explore the genomic diversity…
Introduction Choosing the correct RNA-seq sequencing depth is one of the most important decisions when designing a transcriptomics experiment. Sequencing too few reads can reduce the ability to detect differentially expressed genes, while excessive sequencing…
A practical guide to the bacterial genome assembly pipeline, from raw sequencing reads to polished assemblies and functional genome annotation.
A step-by-step guide to RNA-seq data analysis, from FASTQ quality control to differential gene expression and pathway enrichment.
Learn what is genome annotation, how it works, and which tools are most used. A complete guide to structural and functional genome annotation for beginners.