QIIME 2 Master Interactive Lab
Complete 20-stage interactive workbench for 16S, 18S, and ITS amplicon sequencing. Includes live parameter sync, DADA2 overlap calculator, rarefaction depth advisor, manifest generator, and metadata builder.
- DADA2 Denoising
- Taxonomy Classification
- Core Diversity
- ANCOM-BC
- Live Manifest Gen
SAMtools & BAMtools Suite
Master high-throughput sequence alignment manipulation: view, sort, index, filter, and flagstat BAM/CRAM files. Interactive bitwise flag decoder and depth coverage analyzer.
- SAM / BAM / CRAM Conversion
- Bitwise Flag Decoders
- Coverage Depth Analysis
- Variant Calling (mpileup)
HISAT2 RNA-Seq Alignment
Fast and sensitive splice-aware alignment of RNA-seq reads using Hierarchical Graph FM Indexing. Comprehensive exon-intron junction models and transcriptome indexing.
- Splice-Aware Mapping
- Genome Indexing (HGFM)
- Stranded RNA-Seq
- Junction Detection
Bowtie & Bowtie 2
Ultrafast and memory-efficient alignment of sequencing reads to long reference genomes using Burrows-Wheeler Transform. Optimized for gDNA, ChIP-seq, and ATAC-seq workflows.
- BWT Indexing
- End-to-End vs Local Alignments
- ChIP-seq / ATAC-seq
- Multi-mapping Read Handling
DESeq2 & EdgeR Workbench
End-to-end RNA-Seq differential expression analysis: raw count normalization, variance-stabilizing transformation, dispersion estimation, PCA visualizations, and volcano plots.
- Count Normalization
- Negative Binomial GLMs
- Volcano & Heatmap Plots
- Batch Effect Correction
MaxQuant & MSFragger Lab
Liquid chromatography-mass spectrometry (LC-MS/MS) data science: peptide-spectrum matching, label-free quantification (LFQ), TMT isobaric labeling, and protein network analysis.
- DDA & DIA Analysis
- MaxLFQ & TMT Quant
- Post-Translational Mod (PTMs)
- STRING / Cytoscape Pathways
GATK Best Practices Pipeline
Standardized pipeline for germline and somatic variant discovery: base quality score recalibration (BQSR), HaplotypeCaller, VCF filtering, and functional annotation with SnpEff / ANNOVAR.
- SNV & Indel Discovery
- BQSR Recalibration
- Joint Genotyping
- VCF Filtering & Annotation
Shotgun Assembly & MAG Binning
Reconstruct Metagenome-Assembled Genomes (MAGs) from complex environmental samples using MEGAHIT, SPAdes, MetaBAT2, CheckM quality assessment, and GTDB-Tk phylogenomic taxonomy.
- De Novo Metagenome Assembly
- Tetranucleotide Binning
- CheckM Completeness & Contam
- GTDB-Tk Phylogenetics
AlphaFold & ColabFold Modeling
Predict 3D macromolecular structures from amino acid sequences using AI models. Evaluate per-residue confidence (pLDDT), Predicted Aligned Error (PAE), and multimer protein-protein docking.
- AlphaFold2 / AlphaFold3
- pLDDT & PAE Interpretation
- Protein-Protein Interfaces
- PyMOL / ChimeraX Scripts
Kraken 2 & Bracken Profiler
Ultra-fast k-mer classification and abundance re-estimation for whole-genome shotgun metagenomics. Build custom databases and estimate true species-level relative abundances.
- Exact k-mer Taxonomic Labeling
- Bracken Bayesian Re-estimation
- Custom Database Generation
- Krona / Pavian Visualizations