Discover Databases skills, compare source repositories and read the instructions for each workflow.
Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels. Use when calling germline variants from ONT or PacBio alignments, particularly when high accuracy is needed for clinic...
Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evaluating variant quality, comparing samples, or summarizing VCF contents.
Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.
Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR). Use for produc...
Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate species-level abundances are needed fro...
Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell labeling.
Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample distance heatmaps, and p-value histograms.
Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers. Use when accurate taxonomic profiling is needed and computational resou...
De novo genome assembly from Oxford Nanopore or PacBio long reads using Flye and Canu. Produces highly contiguous assemblies suitable for complete bacterial genomes and resolving complex regions.
Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batches of enzymes, or commercially available enzyme sets. Returns cut positions for linear or cir...
Scaffold contigs into chromosome-level assemblies using Hi-C data with YaHS, 3D-DNA, SALSA2, and validate with BUSCO and contact maps.
Polish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka). Essential for improving long-read assembly accuracy.
Peptide-spectrum matching and protein identification from MS/MS data. Covers database searching, spectral library matching, and FDR estimation using target-decoy approaches.
Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences, creating new sequence files, or outputting modified records.
End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profiling.
Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Covers library-free and library-based workflows for deep proteome profiling.
Quality control for pooled CRISPR screens. Covers library representation, read distribution, replicate correlation, and essential gene recovery. Use when assessing screen quality before hit calling or diagnosin...
End-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyping, and spatial statistics.
Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlaid on histology images.
End-to-end single-cell RNA-seq workflow from 10X Genomics data to annotated cell types. Covers QC, normalization, clustering, marker detection, and cell type annotation.
Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate molecule counting is needed, such as in single-cell RNA-seq, lo...
Visualize enrichment results using enrichplot package functions. Covers dotplot, barplot, cnetplot, emapplot, gseaplot2, ridgeplot, and treeplot for clusterProfiler results.
Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use for parsing Newick, Nexus, PhyloXML, and NeXML tree formats, converting between formats, and handling multiple trees in a single f...
End-to-end workflow for detecting structural variants from long-read sequencing data. Covers ONT/PacBio alignment with minimap2 and SV calling with Sniffles or cuteSV.
The default order uses GitHub repository stars from our indexed data. Stars belong to the source repository and may be shared by multiple skills. They indicate repository interest, not skill installs or an independent quality score.