Browse Tools

Use when performing neuroimaging image registration, brain extraction, cortical thickness analysis, or bias field correction with ANTs (Advanced Normalization Tools). Covers SyN diffeomorphic registra

ART (Artificial Read simulator Tool) simulates next-generation sequencing reads from a reference FASTA for Illumina, 454, and SOLiD platforms. Use when users need to generate synthetic NGS reads for b

ATACseqQC -- R/Bioconductor package for ATAC-seq quality control and assessment. Computes fragment size distribution, nucleosome positioning, TSS enrichment score, library complexity, and signal-to-no

Augur — Nextstrain's Python toolkit for phylogenetic analysis of pathogen genomes. Provides modular subcommands for sequence filtering, multiple alignment, phylogenetic tree building, temporal dating,

Badread simulates long-read sequencing reads (Oxford Nanopore and PacBio) from a reference FASTA with realistic error models, length distributions, chimeras, junk reads, and glitch errors. Use when us

Barrnap (Bacterial Ribosomal RNA Predictor) is a fast command-line tool for predicting ribosomal RNA (rRNA) gene locations in genome sequences using HMMER3/nhmmer profile HMMs. Supports bacteria (bac)

Use when converting Illumina BCL (Binary Base Call) files to FASTQ format using BCL Convert, the successor to bcl2fastq. Supports all modern Illumina platforms including NovaSeq X, NovaSeq X Plus, Nov

bigBedToBed converts bigBed binary indexed files (.bb) back to plain-text BED format. Part of the UCSC Kent utilities (Jim Kent tools). Use when extracting genomic intervals from bigBed files for down

Biopython — foundational Python library for computational molecular biology and bioinformatics. Provides sequence I/O for 30+ formats (FASTA, FASTQ, GenBank, EMBL), NCBI Entrez database access, BLAST

The BLAST+ (Basic Local Alignment Search Tool) suite finds regions of local similarity between sequences. It is the gold standard for sequence similarity searching in bioinformatics. Use this skill to

Use when working with cardrgi — CARD/RGI (Comprehensive Antibiotic Resistance

CasTLE (Cas9 High-Throughput maximum Likelihood Estimator) — empirical Bayesian framework for analyzing pooled CRISPR/Cas9 and RNAi genetic screens. Identifies genes with significant phenotypic effect

CrossMap is a Python tool for genome coordinate liftover — converting genomic positions between different genome assemblies (e.g., hg19 to hg38, GRCh37 to GRCh38, mm9 to mm10). Supports BED, BAM/SAM/C

Deblur is a metagenomics and microbiome tool for denoising 16S rRNA amplicon sequencing data, producing exact sequence variants (ESVs/sOTUs) by applying an error model to demultiplexed single-end read

DeepSignal — deep learning-based 5mC CpG methylation detection from Oxford Nanopore sequencing raw signals. Uses a BiLSTM+Inception neural network trained on bisulfite-seq-labeled data to call methyla

demuxlet and freemuxlet (popscle toolkit) — genotype-based and reference-free demultiplexing of pooled droplet-based single-cell RNA-seq experiments. demuxlet requires known donor genotypes (VCF/BCF)

DIAMOND — fast protein alignment and translated DNA search tool, operating at 100x-10,000x the speed of BLAST. Aligns protein query sequences against protein reference databases (blastp) or translated

Use when working with Dynamo, `dynamo-release`, or transcriptomic vector field analysis for single-cell RNA-seq, metabolic labeling, and multi-omics time-course data. Dynamo estimates RNA velocity wit

EcoPCR performs in silico PCR simulation on reference sequence databases to evaluate primer specificity and predict amplified taxa for metabarcoding studies. Part of the OBITools suite for environment

Use when working with eggnog-mapper — eggNOG-mapper — fast functional

Use when working with encyclopedia — encyclopeDIA — Java-based DIA (Data-Independent

EPACTS (Efficient and Parallelizable Association Container Toolbox) — rare variant association testing toolkit for whole-genome and whole-exome sequencing studies. Supports single-variant tests (score

f5c — ultra-fast methylation calling and event alignment for Oxford Nanopore sequencing data. Re-implements nanopolish call-methylation and eventalign with multi-threading and optional CUDA GPU accele

FLAIR — Full-Length Alternative Isoform analysis of RNA for long-read sequencing. Corrects, defines, and quantifies transcript isoforms from nanopore cDNA, native RNA, and PacBio reads. Provides splic

FreeSurfer is a neuroimaging software suite for processing and analyzing human brain MRI data. Use for cortical surface reconstruction, brain parcellation, volumetric segmentation, cortical thickness

GATK-SV — Broad Institute WDL pipeline for end-to-end structural variant (SV) discovery, genotyping, and filtering from short-read whole-genome sequencing. Detects deletions, duplications, inversions,

Genrich — peak caller for genomic enrichment assays (ChIP-seq and ATAC-seq) with built-in support for multiple biological replicates via Fisher's method, multimapping reads with fractional pileup coun

GetOrganelle assembles organelle genomes (chloroplast, mitochondria, ribosomal DNA) from whole-genome sequencing reads. Supports embryophyte plastomes, plant/animal/fungal mitochondria, and target-enr

Use when working with ggCaller — a genome graph-based gene caller for bacterial pangenomics. Calls open reading frames (ORFs) across multiple bacterial genomes simultaneously using a colored compacted

GlimmerHMM — ab initio eukaryotic gene finder using a generalized hidden Markov model (GHMM). Predicts gene structures (exons, introns, UTRs, splice sites) in eukaryotic genome sequences from FASTA in

GMAP/GSNAP — splice-aware genomic alignment suite for mRNA, cDNA, EST, and short-read sequences. GMAP maps long cDNA/mRNA/EST sequences to a genome and identifies intron boundaries, alternative splici

GRIDSS (Genomic Rearrangement IDentification Software Suite) is a modular structural variant and breakend caller for Illumina short-read data that combines alignment-guided positional de Bruijn graph

HiC-Pro is an all-in-one pipeline for processing Hi-C sequencing data from raw FASTQ files to normalized contact matrices. Performs read alignment with Bowtie2, restriction-fragment assignment, valid-

HiGlass — web-based genome browser and visualization platform for multi-resolution

HOMER (Hypergeometric Optimization of Motif EnRichment) — a comprehensive suite of tools for motif discovery and next-generation sequencing analysis. HOMER performs de novo motif finding optimized for

Genome assembly and pangenome analysis tools used by the Human Pangenome Reference Consortium (HPRC). Use this skill for haplotype-resolved assembly with hifiasm or Verkko, telomere-to-telomere (T2T)

Use when polishing a genome assembly with short reads (Illumina) or a combination of short and long reads (PacBio, Oxford Nanopore). HyPo is a fast hybrid polisher that corrects base-level errors in d

Immcantation — integrated software suite for adaptive immune receptor repertoire (AIRR-seq) analysis of B-cell and T-cell receptors. Covers the full pipeline from raw FASTQ preprocessing (pRESTO) thro

Use when working with indexcov — a fast BAM/CRAM coverage estimator from the goleft suite. Reads only BAM index (.bai) files rather than raw reads, enabling coverage QC across hundreds of samples in m

IsoQuant — long-read RNA-seq transcript discovery and quantification tool from PacBio and Oxford Nanopore data. Assigns reads to known isoforms, discovers novel transcripts via intron graph algorithms

Use when working with ldsc (LD Score Regression) — a command-line Python tool for estimating SNP heritability and genetic correlations from GWAS summary statistics using linkage disequilibrium score r

LIMIX — Python library for linear mixed models (LMM) and interaction QTL (iQTL) mapping. Use for eQTL discovery, cis-QTL and trans-QTL scans, GxE interaction testing, conditional QTL analysis, and GWA

Mamba and Micromamba package and environment management for conda-based bioinformatics workflows. Use this skill to create reproducible environments, install Bioconda and conda-forge packages, run com

Use this skill for Manta structural-variant calling from paired-end short-read BAM or CRAM files, including germline (`--bam`), tumor/normal somatic (`--tumorBam` + `--normalBam`), exome (`--exome`),

mapDamage2 routing skill for ancient DNA damage pattern analysis. Use this skill when users mention mapDamage2, mapDamage, ancient DNA, aDNA, DNA damage patterns, C-to-T substitutions, deamination, po

MethylDackel (formerly PileOMeth) -- fast C tool for extracting per-base methylation metrics from coordinate-sorted BAM/CRAM files produced by bisulfite sequencing aligners (Bismark, bwa-meth, BSMAP).

methylKit -- R/Bioconductor package for DNA methylation analysis from bisulfite sequencing data. Reads Bismark, BSmap, and generic CpG coverage files. Provides differential methylation analysis at bas

miRDeep2 — de novo microRNA (miRNA) discovery and quantification from small RNA-seq data. Identifies known and novel miRNAs by mapping collapsed reads to the genome, scoring hairpin structures, and co

MycoCLAP (Mycological Characterized and Listed Annotated Proteins) is a manually curated database of biochemically characterized fungal proteins from primary literature. Use when annotating fungal pro

netCDF4 is the Python and NumPy interface to the netCDF C library for reading, writing, querying, and validating NetCDF and OPeNDAP datasets. Use this skill for low-level `Dataset` and `Variable` work