Browse Tools

Bismark — bisulfite-seq alignment and methylation calling toolkit. Maps bisulfite-treated reads to a reference genome using Bowtie 2, HISAT2, or minimap2, performs cytosine methylation calls in CpG/CH

Chopper — fast Rust-based quality, length, and GC content filtering and trimming tool for long-read sequencing data (Oxford Nanopore, PacBio) in FASTQ format. Successor to NanoFilt with multithreaded

cuteSV -- sensitive and scalable long-read-based structural variation (SV) detection from PacBio CLR, PacBio CCS/HiFi, and Oxford Nanopore Technology (ONT) sequencing data. Detects deletions, insertio

deepTools — suite of Python tools for efficient analysis and visualization of high-throughput sequencing data including ChIP-seq, ATAC-seq, MNase-seq, and RNA-seq. BAM-to-bigWig conversion with normal

Use when working with falco — a high-speed C++ reimplementation of

fastp — ultra-fast all-in-one FASTQ preprocessor for quality control, adapter trimming, quality filtering, per-read trimming, polyG/polyX removal, UMI processing, base correction, deduplication, and c

MAFFT — multiple sequence alignment for nucleotide and protein sequences. Implements progressive (FFT-NS-1, FFT-NS-2), iterative refinement (FFT-NS-i), and consistency-based iterative methods (L-INS-i

NanoFilt — Python tool for filtering and trimming Oxford Nanopore long-read sequencing data in FASTQ format. Filters reads by minimum average quality score, minimum/maximum read length, and GC content

NanoPlot — visualization and quality-control tool for Oxford Nanopore long-read sequencing data. Generates read length histograms, quality distribution plots, cumulative yield curves, and alignment id

pbmm2 — SMRT C++ wrapper for minimap2's C API providing native PacBio long-read alignment. Supports CCS/HiFi, SUBREAD, ISOSEQ, and UNROLLED presets. Reads native PacBio BAM and dataset XML inputs, pro

Pharokka — fast, scalable bacteriophage genome annotation. Annotates phage genomes using pyhmmer (PHROGs), MMseqs2 (CARD, VFDB, COG), and tRNAscan-SE. Produces GenBank, GFF3, and tabular outputs in mi

Prodigal/Pyrodigal — prokaryotic gene prediction tools that identify protein-coding sequences (CDS) in bacterial and archaeal genomes and metagenomes using dynamic programming. Prodigal is the canonic

RSEM (RNA-Seq by Expectation-Maximization) — accurate gene and isoform quantification from RNA-seq data using EM algorithm with probabilistic multi-mapped read assignment. Supports STAR, Bowtie2, and

somalier -- fast sample-identity verification and relatedness checking for BAM/CRAM/VCF/GVCF files. Extracts genotypes at informative polymorphic sites, computes pairwise relatedness using bit-vector

trimAl — automated alignment trimming tool for removing spurious sequences and poorly aligned regions from multiple sequence alignments. Supports automated heuristic methods (gappyout, strict, strictp

VCFtools — C++ toolkit for filtering, comparing, summarizing, converting, and manipulating VCF (Variant Call Format) and BCF files. Provides site and individual-level filtering, allele frequency calcu

scikit-allel — Python package for exploratory analysis of large-scale genetic variation data. Provides data structures for genotypes, haplotypes, and allele counts (GenotypeArray, HaplotypeArray, Alle

Zarr — chunked, compressed N-dimensional arrays for Python with cloud-native storage. Provides hierarchical groups, pluggable compression codecs (Blosc, Zstd, Gzip), sharding for large-scale datasets,

Use when working with aurora — a machine learning GWAS R package for identifying microbial habitat adaptation genes and autochthonous strain provenance. Implements a Random Forest + random-walk (AUtoc

Bambi (BAyesian Model-Building Interface) is a high-level Python package for fitting Bayesian generalized linear and generalized linear mixed models using a concise, R-style Wilkinson formula syntax.

CoralNet is a web platform for benthic image analysis, serving as a repository and resource. It uses deep learning for automated annotation of benthic images, reducing the manual inspection bottleneck

Dandelion (sc-dandelion) is a Python package for single-cell BCR and TCR immune repertoire analysis integrated with scanpy. Processes 10x Genomics VDJ output (filtered_contig_annotations.csv, airr_rea

DoE.base is a foundational R package by Ulrike Groemping for full factorial experimental designs and designs based on orthogonal arrays. It provides utility functions for the shared `design` class use

EpiEstim — CRAN R package from the MRC Centre for Global Infectious Disease Analysis for estimating the time-varying (instantaneous) reproduction number R_t from epidemic incidence time series. Implem

Use when working with Escher for metabolic pathway visualization, map editing, data overlay, or embedding interactive maps in notebooks and web pages. Covers the browser Builder and Viewer, the Python

fdrtool — estimation of tail area-based false discovery rates (Fdr/q-values) and density-based local false discovery rates (fdr) from observed test statistics. Supports four null models: normal (z-sco

Finlay is a fast Triangle-Free Solver for undirected graphs, part of the Aegypti project. It detects, counts, and lists triangles in graphs provided in DIMACS or Boolean Adjacency Matrix formats. It p

HDMT — High-Dimensional Mediation Testing for joint significance of exposure-mediator and mediator-outcome associations. Controls FWER and FDR for mediation hypotheses in high-dimensional settings (ep

Hmsc (Hierarchical Modelling of Species Communities) is an R package for fitting joint species distribution models (JSDMs) in a Bayesian hierarchical framework. It links species occurrences or abundan

qvalue — Q-value estimation for false discovery rate control in multiple hypothesis testing. Estimates q-values, the proportion of true null hypotheses (pi0), and local false discovery rates from vect

Reactome — curated pathway knowledgebase and analysis platform for pathway enrichment, expression overlay, and species comparison. Use when user needs pathway over-representation analysis (ORA) with R

REDCap (Research Electronic Data Capture) is a secure, web-based application for building and managing online surveys and databases, widely used in clinical and translational research. This skill cove

rootwater is a Python toolbox for estimating root water uptake (RWU) from diurnal soil moisture dynamics in the rhizosphere, with complementary tools for converting sap velocity to sap flow in active

t-SNE via Rtsne — Barnes-Hut t-distributed Stochastic Neighbor Embedding for nonlinear dimensionality reduction and visualization. Wraps Van der Maaten's C++ Barnes-Hut implementation for O(n log n) c

Scanpy — scalable Python toolkit for analyzing single-cell gene expression data built on AnnData. Provides preprocessing (QC, normalization, feature selection, dimensionality reduction), clustering (L

Query STRING API for protein-protein interaction networks, functional enrichment, and interaction partner discovery. Covers 59M proteins across 5000+ species with 20B+ scored interactions from 7 evide

Cenote-Taker 3 is a comprehensive bioinformatics pipeline for the discovery and annotation of diverse viral genomes (the virome) from metagenomic assemblies or individual sequences. It identifies vira

TCGAbiolinks for searching, downloading, and analyzing cancer genomics data from the NCI Genomic Data Commons (GDC). Routes tasks for GDCquery/GDCdownload, data preparation with GDCprepare, differenti

Uni-Mol universal 3D molecular representation learning framework for molecular property prediction, protein-ligand docking, drug-target interaction, and binding affinity scoring. Covers unimol_tools P

windspharm — high-level Python library for global wind field computations on the sphere using spherical harmonic transforms (SPHEREPACK). Compute vorticity, divergence, stream function, velocity poten

xclim is an xarray-based climate analytics library for computing climate indicators and indices, running data quality checks, managing ensembles, and batch-processing netCDF datasets from the command

Use when working with abricate — ABRicate — mass screening of contigs

slow5lib and blue-crab — C library and Python tools for reading, writing, and converting Oxford Nanopore raw signal data in SLOW5/BLOW5 format. blue-crab converts between FAST5, POD5, and SLOW5/BLOW5

Use when working with xMIP (formerly cmip6_preprocessing) — a Python package designed to make CMIP6 (Climate Model Intercomparison Project Phase 6) data "analysis-ready" by homogenizing inconsistent n

Use when working with ACE (Accurate CRISPR Essentiality) — a Python package from the Pe'er Lab (Memorial Sloan Kettering) for estimating gene essentiality from CRISPR pooled knockout screens. Models g

Cell Ranger — 10x Genomics official analysis pipeline for Chromium single-cell and spatial data. Performs FASTQ generation, alignment (STAR-based), barcode processing, UMI counting, V(D)J assembly, Fe

ClonalFrameML (CFML) — maximum-likelihood inference of recombination in bacterial genomes. Detects horizontally transferred genomic segments, estimates recombination parameters (R/theta, nu, delta), a

EDTA (Extensive de-novo TE Annotator) — automated transposable element annotation pipeline for plant genomes. Integrates LTRharvest, LTR_FINDER, TIR-Learner, Helitron-Scanner, and RepeatMasker into a

MEGAHIT — ultra-fast and memory-efficient NGS assembler for large and complex metagenomes, single genomes, and single-cell data. Uses succinct de Bruijn graph (SdBG) with an iterative multi k-mer stra

SPAdes — de Bruijn graph genome assembler for Illumina, IonTorrent, and hybrid short+long read data. Modes: isolate (--isolate), metagenomics (--meta), single-cell MDA (--sc), plasmid recovery (--plas