My Skills
Exome & Whole-Genome Sequencing
- Raw data QC
- FastQC, Falco, RabbitQCPlus, Fastp, Trim Galore, Cutadapt, FASTX-Toolkit, UMI-tools, Fgbio, FastQ Screen, Find-adapt, MultiQC
- Alignment
- Bowtie2, Bowtie, BWA, BWA-MEME, bwa-mem2, Minimap2
- Post alignment QC
- Bedtools, Picard, MultiQC, SAMstats
- Mark/Remove PCR/Optical duplicates
- GATK, Picard, Sambamba
- Base quality score recalibration
- GATK
- Coverage analysis
- Mosdepth, Pandepth, Megadepth, Bamtocov, Qualimap
- Variant calling (SNV/Indels)
- GATK HaplotypeCaller, DeepVariant, Bcftools, FreeBayes, VarScan2, Strelka2, GATK Mutect2
- Structural Variants (SVs)
- Manta, Delly, LUMPY, GRIDSS, SVABA, CNVnator, CNVkit, ExomeDepth
- Variant Quality Score Recalibration (VQSR)
- GATK
- Variant normalisation
- Vt, Bcftools
- Variant QC/statistics
- Vcfstats, RTG Tools, Vcflib, DISCVRSeq
- Variant filtering
- Bcftools, Vcftools
- Variant Annotation
- ANNOVAR, VEP, OpenCRAVAT, SnpEff & SnpSift
- Relevant databases and resources
- Population frequency database
- Genome Aggregation Database (gnomAD), dbSNP, NCBI ALFA, Kaviar, allofus, ABraOM, GME Variome, 61KJPN-SNV/INDEL, KOVA, almena, IndiGenomes, GenomeAsia, NCVD
- Disease relevant database
- LOVD, COSMIC, Orphanet, OMIM, DECIPHER, ClinVar, HGMD®, OncoKB, CIViC, CancerMine, ClinPGx, CPIC, ClinGen, GeneReviews, MedGen, HPO, GeDiPNet, SysNDD, MyGene2, Pubcasefinder, Matchmaker, PhenomeCentral, GenCC, MGeND
- Population frequency database
GWAS Analysis Workflow
- Quality Control (QC)
- PLINK, KING, HAIL, QCtools
- Population Structure
- PCA (EIGENSOFT), fastPCA, ADMIXTURE
- Association Testing
- PLINK, SNPTEST, GEMMA, BOLT-LMM, Regenie, SAIGE
- Imputation
- Minimac4, Beagle, IMPUTE5, SHAPEIT, Eagle
- Meta-analysis
- METAL, METASOFT, GWAMA, mvGWAMA
- Visualization
- Manhattan plot, QQ plot, LocusZoom, GWAS-VCF Browser, Circos
RNA-seq Workflow
- Raw data QC
- FastQC, Falco, RabbitQCPlus, FindAdapt, Fastp, Trim Galore, Cutadapt, FASTX-Toolkit, UMI-tools, Fgbio, FastQ Screen, MultiQC
- Alignment
- STAR, HISAT2, TopHat2; Salmon, Kallisto
- Post alignment QC
- dupRadar, RSeQC, Qualimap, RNA-SeQC
- Gene/Transcript Quantification
- featureCounts, HTSeq-count, Salmon, Kallisto, StringTie
- Normalization
- DESeq2, edgeR, Limma-Voom, Ballgown, EDASeq
- Sample QC/EDA
- PCA Plot, MDS Plot, Sample correlation analysis, Hierarchical clustering
- Remove batch effect
- SVA, RUVseq, ComBat-Seq, removeBatchEffect-limma, reComBat, bapred
- Diagnostic plot
- MA plot, Dispersion plot, Histogram of the p-value
- Gene Set/Pathway Analysis
- GOseq, topGO, clusterProfiler, Gprofiler2, Enrichr, DAVID, WebGestaltR, GSEA, GSVA, SPIA, EnrichmentBrowser
- Network/Regulatory analysis
- NetworkAnalyst, iRegulon, Cytoscape, GeneMANIA, STRING, GENIE3, SCENIC, Inferelator, Arboreto, TRIAGE
- Co-expression Modules Identification
- CEMiTool, WGCNA, PyWGCNA, multiWGCNA, BioNERO, GWENA
- RNA fusion detections
- nf-core/rnafusion, FUNGI, CICERO, TrinityFusion, AGFusion, STAR-Fusion, FusionCatcher, Arriba, ChimeraScan, EricScript, SoapFuse
- Splicing / Isoform
- LeafCutter, rnasplice, Splam, rMATS turbo v4.3.0, rmats2sashimiplot, TranD, betAS, SpliceWiz, RiboSplitter, mkcDBGAS, DICAST, SpliceTools, SpliceVault, ELLIPSIS, MISO, MAJIQ, SUPPA2, SplAdder, MOCCASIN
- Variant calling
- GATK, MuTect2, Samtools, VarScan2, Varikondo, SuperFreq
- Circular RNA identification
- CirComPara2, CIRCexplorer2, CIRIquant, CIRI2, CircAST, Circall, circrna, Circtools, CRAFT, AQUARIUMHB
- Cell-free RNA
- RARE-Seq, cfRNA-SEEK, cfPeak, cfOmics, FastNeo, exceRpt
- Immune Repertoire Analysis
- RIMA, TRUST4, MiXCR, Immunarch, nf-core/airrflow
- Immune Infiltration Analysis
- RIMA, CIBERSORT, TIMER, quanTIseq, xCell, EPIC, MCP-counter
- Immune Response
- TIDE (Tumor Immune Dysfunction and Exclusion)
- Microsatellite instability (MSI)
- MSIsensor2, MANTIS, MSIsensor-RNA, mSINGS
- HLA type identification
- arcasHLA, HLAProfiler, seq2HLA, OptiType, PHLAT, ImMunoGeneTics (IMGT) database
- Neoantigen Identification
- pVACtools
Post-GWAS Analysis Workflow
- Fine-mapping
- FINEMAP, SuSiE, PAINTOR, CAVIAR
- Colocalisation
- COLOC, eCAVIAR, HyPrColoc
- Mendelian Randomization
- TwoSampleMR, MR-Base, GSMR, CAUSE
- Meta-analysis
- METAL, METASOFT, GWAMA, mvGWAMA
- Pleiotropy Analysis
- CPASSOC, PLACO, GPA, ASSET
- Functional Annotation
- ANNOVAR, VEP, FUMA, OpenCRAVAT, SNPnexus, RegulomeDB
- Pathway & Gene-set Analysis
- MAGMA, DEPICT, GSEA, Pascal, INRICH, WebGestaltR, Enrichr
- Genetic Correlation & Heritability
- LDSC, GCTA, BOLT-REML
- Polygenic Risk Score (PRS) Analysis
- PRSice, LDpred, SBayesR, PLINK