Sudipta Sardar is a co-founder of BioUnfold and a bioinformatics researcher at Pusan National University. He builds BioUnfold's courses and writes its guides on sequence analysis, genomics workflows, and the tools bioinformaticians use every day — with a focus on making the field approachable for beginners.
Courses
Bioinformatics Databases
Structural Bioinformatics
Metagenomics Fundamentals
ML for Biology
Phylogenetics & Evolution
RNA-Seq Data Analysis
R for Bioinformatics
Protein Structure Prediction
Linux for Bioinformatics
Molecular Docking Basics
Genomics 101
Python for Biologists
Introduction to Bioinformatics
Articles
Awk, Sed, and Bash One-Liners Every Bioinformatician Should Know
A working cheat sheet of awk, sed, grep, and bioawk one-liners for FASTA, FASTQ, VCF, BED, and SAM files, with the syntax explained line by line.
Reading BLAST Results: E-values, Bit Scores, and Query Coverage
Learn to read a BLAST hit table like a bioinformatician: what E-value really measures, why bit score beats raw score, and how coverage prevents false hits.
Bottom-Up Proteomics Explained: From Digested Peptides to Protein IDs
How shotgun proteomics works end to end: trypsin digestion, LC separation, MS1/MS2 acquisition, peptide spectrum matching, and protein inference.
Cell-Type Annotation in scRNA-seq: Markers vs CellTypist, Azimuth, and SingleR
A decision tree for annotating single-cell clusters using marker scoring, SingleR, Azimuth, and CellTypist — and when to trust each call.
Peak Calling with MACS3: How ChIP-seq and ATAC-seq Peaks Are Found
How MACS3 turns aligned reads into peaks: fragment size estimation, local lambda background, and the Poisson test behind narrow vs broad calling.
Conda Environments, Channels & Isolation: The Bioinformatics Setup That Prevents Conflicts
A beginner guide to conda environments, bioconda channels, strict priority, and the libmamba solver for conflict-free bioinformatics on Apple Silicon Macs.
De Novo Genome Assembly with Flye and hifiasm: A Practical Walkthrough
Assemble a genome from scratch with Flye for ONT reads or hifiasm for PacBio HiFi, when Canu still wins, and how to read the assembly graph.
Bisulfite Sequencing Explained: From Raw Reads to Methylation Calls with Bismark
How bisulfite chemistry turns unmethylated C into T, why it breaks ordinary aligners, and how Bismark and methylKit call per-CpG methylation and DMRs.
Docker vs Singularity/Apptainer: Choosing a Container Tool for Bioinformatics
Why HPC clusters ban Docker's root daemon, how Apptainer's rootless .sif images fix it, and how to pull or convert a container image for the cluster.
Downloading Sequencing Data from SRA and ENA: prefetch and fasterq-dump
A step-by-step guide from an SRA accession to usable FASTQ files, using prefetch + fasterq-dump plus faster ENA FTP and Aspera shortcuts.
FASTA and FASTQ Explained: Sequence Files and Phred Quality Scores
How FASTA stores sequences, how FASTQ adds a fourth line of per-base Phred quality, and why Q30 means 99.9% base-call accuracy.
GO, KEGG, and GSEA Enrichment with clusterProfiler in R
Turn a DESeq2 results table into biological insight with clusterProfiler: ID conversion, enrichGO, enrichKEGG, gseKEGG, and dotplot/cnetplot visualization.
Setting Up a Protein-Ligand MD Simulation in GROMACS: Step by Step
A hands-on GROMACS tutorial for protein-ligand MD: topology with CHARMM36/CGenFF, solvation, minimization, NVT/NPT equilibration, and production.
How Read Aligners Work: Mapping Reads to a Reference Genome
Inside BWA-MEM, Bowtie2, and HISAT2: how the Burrows-Wheeler Transform, FM-index, and seed-and-extend map millions of reads in minutes.
How to Install Anaconda on macOS (and When to Choose It Over Miniconda)
A beginner guide to installing Anaconda Distribution on Apple Silicon macOS, plus an honest Anaconda-vs-Miniconda decision for bioinformatics work.
Install AutoDock Vina with Conda on Apple Silicon (the Right Way)
Install AutoDock Vina on an Apple Silicon Mac the right way: skip the broken bioconda 1.1.2 build and use the native arm64 conda-forge vina 1.2.7 package.
Install bedtools with Conda: Genome Arithmetic on Apple Silicon
Install bedtools 2.31.1 natively on Apple Silicon with conda and bioconda in a tiny isolated env, then verify it with a quick genome arithmetic smoke test.
Install Biopython in a conda Environment (macOS, Apple Silicon)
Install Biopython in an isolated conda environment on Apple Silicon, verify the native arm64 build, and parse a FASTA file with SeqIO.
Install NCBI BLAST+ Locally with Conda for Offline Sequence Search
Beginner guide to installing NCBI BLAST+ on an Apple Silicon Mac with conda, in one isolated env, then verifying blastn and building a database offline.
Install BWA and Bowtie2 Read Aligners with Conda (Apple Silicon)
Install BWA and Bowtie2 short-read aligners together in one conda env on an Apple Silicon Mac, with native arm64 builds, verify steps, and fixes for common errors.
Install DESeq2 and edgeR via conda (R/Bioconductor, Apple Silicon)
Build a pinned R and Bioconductor stack with DESeq2 and edgeR inside one isolated conda environment on Apple Silicon, never touching system R.
Install fastp and Trimmomatic for Read Trimming (macOS, conda)
Install fastp and Trimmomatic on macOS with conda, then run a real adapter- and quality-trimming command with each read trimmer.
Install FastQC and MultiQC on macOS (Apple Silicon) with conda
Set up FastQC and MultiQC in one conda env on Apple Silicon to QC every FASTQ file and roll the results into a single dashboard report.
Install GATK4 with Conda for Variant Calling (macOS Apple Silicon)
Install GATK4 4.6.2.0 natively on an Apple Silicon Mac with conda, isolate it in its own environment, run the gatk wrapper, and fix common bioconda errors.
Install IGV and igvtools to View BAMs and VCFs Locally (macOS, conda)
Launch the IGV desktop genome browser from a conda env, index BAM and VCF files with igvtools, and browse alignments and variants offline.
Install MAFFT and IQ-TREE for Phylogenetics (macOS, conda)
Install MAFFT and IQ-TREE 2 in one conda env, align a gene family, then infer a maximum-likelihood tree with ModelFinder and ultrafast bootstrap.
How to Install Miniconda on macOS (Apple Silicon): A Beginner's Guide
Install Miniconda on Apple Silicon the native arm64 way, set up conda-forge and bioconda channels, and sidestep the Anaconda defaults Terms of Service gate.
Install Nextflow with Conda for Reproducible Pipelines (Apple Silicon)
Install Nextflow 26.04.6 in an isolated conda env on Apple Silicon macOS with bioconda channels, a native arm64 JDK, and a working hello-world smoke test.
Install Open-Source PyMOL with Conda for Molecular Visualization (Apple Silicon)
Install open-source PyMOL 3.1.0 with conda on an Apple Silicon Mac using one isolated env, native arm64 builds, and a real headless smoke test to verify it.
Install RDKit for Cheminformatics with Conda (macOS Apple Silicon)
Install RDKit natively on Apple Silicon with conda from the conda-forge channel in an isolated env, then verify it by parsing an aspirin SMILES string.
Install Salmon for RNA-seq Quantification with Conda (Apple Silicon)
Install Salmon 2.3.4 for RNA-seq transcript quantification on an Apple Silicon Mac using an isolated conda env with native arm64 bioconda builds.
Install samtools & bcftools with Conda (macOS Apple Silicon)
Install samtools and bcftools on an Apple Silicon Mac using an isolated conda env with conda-forge and bioconda, then verify with a real BAM smoke test.
Install Scanpy for Single-Cell Analysis with Conda (Apple Silicon)
Install Scanpy 1.12.2 in an isolated conda environment on an Apple Silicon Mac, with native arm64 packages, Leiden clustering support, and a real smoke test.
Install seqkit and seqtk: FASTA/FASTQ Toolkits (macOS, conda)
Install seqkit and seqtk in one conda env on Apple Silicon, then filter, subsample, convert, and get instant stats on FASTA/FASTQ files.
Install Snakemake with Conda for Workflow Management (Apple Silicon)
Install Snakemake on an Apple Silicon Mac with conda: create an isolated env, pin snakemake-minimal, run a one-rule Snakefile, and fix common channel errors.
Install STAR and HISAT2 RNA-seq Aligners (macOS, Apple Silicon, conda)
Install STAR and HISAT2, the two dominant splice-aware RNA-seq aligners, via conda on Apple Silicon, with genome indexing and RAM limits.
Install Subread (featureCounts) and HTSeq for RNA-seq Read Counting (conda)
Install featureCounts (Subread) and htseq-count (HTSeq) in one conda env, then turn STAR or HISAT2 BAM files into a gene counts table for DESeq2.
Untargeted Metabolomics: From LC-MS Data to Pathways With XCMS and MetaboAnalyst
A practical walkthrough of untargeted metabolomics: peak picking in XCMS, feature-table QC and statistics in MetaboAnalyst 6.0, and pathway annotation.
How Molecular Dynamics Simulation Works: Force Fields to Trajectories
A conceptual walkthrough of an MD run: force fields, energy minimization, NVT/NPT equilibration, and production dynamics in GROMACS, AMBER, and OpenMM.
Needleman-Wunsch vs Smith-Waterman: How Pairwise Alignment Works
A step-by-step walk through the dynamic-programming matrices behind global and local alignment, plus a clear rule for when to reach for each.
How MHC/HLA Binding Prediction Works: NetMHCpan and MHCflurry Explained
How MHC/HLA binding prediction works: the peptide groove, anchor residues, and running NetMHCpan-4.2 and MHCflurry 2.2 to interpret %rank and IC50.
NGS Read Quality Control and Trimming with FastQC, fastp, and MultiQC
Learn to read FastQC quality reports, trim adapters and low-quality bases with fastp, and roll up per-sample results with MultiQC.
Oxford Nanopore vs PacBio HiFi: Choosing a Long-Read Sequencing Platform
Compare ONT R10.4.1 with Dorado against PacBio HiFi on accuracy, read length, cost, and use cases so you pick the right platform before assembling.
PLINK File Formats Explained: BED/BIM/FAM vs PGEN/PVAR/PSAM
A column-by-column guide to PLINK 1.9's .bed/.bim/.fam trio and PLINK2's native .pgen/.pvar/.psam, plus how to convert between them and VCF.
Polygenic Risk Scores Explained: From GWAS Summary Stats to PRS
How a polygenic score is a weighted sum of risk alleles, and how to compute one with PRSice-2 clumping+thresholding, LDpred2 shrinkage, and PLINK2 --score.
PPI Networks: From the STRING Database to Cytoscape Visualization
Query STRING v12.5 with a gene list, understand confidence scores and evidence channels, then import the network into Cytoscape for clustering.
Beyond AlphaFold2: Choosing Between AlphaFold3, ESMFold, RoseTTAFold2, and Boltz
A practical guide to AlphaFold3, ESMFold, RoseTTAFold2, and Boltz, comparing speed, complex support, and licensing to pick the right predictor.
Build a Reproducible Bioinformatics Pipeline with Snakemake
Write a real Snakefile with rule all, wildcards, a config.yaml sample sheet, and per-rule conda envs, then inspect the DAG before you run it.
SAM and BAM Files Explained: FLAGs, CIGAR Strings, and samtools
Decode the 11 SAM columns, bitwise FLAG bits, and CIGAR operations behind every alignment file, then inspect them with samtools view and flagstat.
Somatic vs Germline Variant Calling: Tumor-Normal Pairs with Mutect2
Why somatic calling needs a different statistical model than germline, plus a real Mutect2 tumor-normal run from BAM to a filtered somatic VCF.
Spatial Transcriptomics Explained: Visium, Xenium, and Analyzing Tissue in Situ
How Visium, Xenium, and other platforms map gene expression onto intact tissue, and the Squidpy/Seurat workflow for QC, segmentation, and spatial genes.
Variant Annotation and ACMG Classification: From VCF to Clinical Meaning with VEP
Why a raw VCF is clinically meaningless until annotated, how VEP, ANNOVAR, and SnpEff add evidence, and how it maps onto ACMG's five-tier classification.
Variant Calling Explained: From Aligned Reads to a VCF
How a sorted BAM becomes a VCF: pileups, allele depth, spotting sequencing errors, and what HaplotypeCaller, bcftools call, and DeepVariant each do.
Variant Calling from FASTQ to VCF with GATK4 Best Practices
A command-by-command GATK4 tutorial: BWA-MEM alignment, MarkDuplicates, BQSR, HaplotypeCaller, and hard-filtering to a clean germline VCF.
The VCF File Format Explained: From CHROM/POS to GT, DP, and GQ
A field-by-field guide to the VCF format: meta-information lines, the 8 fixed columns, and how FORMAT encodes genotype calls with GT, DP, GQ, and AD.
WGCNA Explained: Building Gene Co-Expression Networks and Finding Modules
How WGCNA turns an expression matrix into gene co-expression modules using soft-thresholding, TOM, and eigengenes linked to sample traits.
Machine Learning in Drug Discovery: From Molecules to Medicine
How machine learning is accelerating drug discovery, from molecular property prediction to generative chemistry and clinical trial optimization.
Single-Cell RNA-Seq: Understanding Cellular Heterogeneity
An introduction to single-cell RNA sequencing, how it differs from bulk RNA-Seq, and the computational tools used to analyze single-cell data.
The AlphaFold Revolution: How AI Solved Protein Structure Prediction
How DeepMind's AlphaFold transformed structural biology, what it means for drug discovery, and how you can use it in your own research.
What Is Bioinformatics? A Beginner's Guide to the Field
An accessible introduction to bioinformatics, covering what it is, why it matters, and how biology and computer science converge to solve modern scientific challenges.