Browse Tools

medaka -- neural network-based tool from Oxford Nanopore Technologies for creating consensus sequences and calling variants from nanopore sequencing data. Polishes draft assemblies from Flye, miniasm,

MEME Suite — comprehensive motif analysis toolkit for DNA, RNA, and protein sequences. Provides de novo motif discovery (MEME, STREME), motif scanning (FIMO), motif comparison (TOMTOM), motif enrichme

Merqury — reference-free quality, completeness, and phasing assessment for genome assemblies using k-mer databases built from Illumina reads. Computes QV (Phred-scaled quality value), k-mer completene

MetaBAT2 — adaptive binning of metagenomic contigs using empirical probabilistic distances of genome abundance and tetranucleotide frequency. Clusters assembled contigs into genome bins (MAGs) from me

metaSPAdes — de novo metagenomic assembler from the SPAdes suite using iterative de Bruijn graphs with multiple k-mer sizes optimized for uneven-coverage metagenomes. Assembles short-read (Illumina pa

MetaWRAP — flexible pipeline for genome-resolved metagenomic data analysis. Wraps read QC (trimming, host removal), metagenomic assembly (MEGAHIT, metaSPAdes), binning (MaxBin2, metaBAT2, CONCOCT), bi

Mikado -- Python pipeline for selecting the best transcript models from multiple RNA-seq assemblies. Merges transcript sets from StringTie, Trinity, CLASS2, and other assemblers, then scores and filte

Miniasm — ultrafast OLC (overlap-layout-consensus) assembler for long reads (PacBio, Oxford Nanopore). Produces unitig-level assemblies from read overlaps computed by minimap2, without error correctio

Use when building phylogenetic trees from genomic sequences using minimap2 for all-vs-all alignment and pairwise distance computation. Covers minimap2 PAF output, distance matrix construction, tree in

Use when working with minipolish — Racon-based polishing of miniasm long-read genome assemblies. Accepts raw nanopore or PacBio reads (FASTQ/FASTA) and a miniasm GFA assembly, runs iterative minimap2

Use when working with MIP (Medical Information Process) — a workflow management system for clinical whole-genome and whole-exome sequencing analysis. Runs end-to-end rare disease (rd_dna, rd_rna) and

MMseqs2 — ultra-fast protein and nucleotide sequence searching, clustering, and taxonomy assignment. Performs all-vs-all comparisons, iterative profile searches, linclust linear-time clustering, easy-

modkit — Oxford Nanopore Technologies Rust CLI for modified base (methylation) analysis on nanopore sequencing data. Processes modBAM files (BAM with MM/ML tags) to compute per-position modification f

Mustache — multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps using scale-space representation. Identifies loops across resolutions from 10 kb down to 500 bp using computer-vi

Mutect2 -- GATK somatic short variant caller for detecting SNVs and indels in tumor samples. Supports tumor-only and tumor-normal paired calling modes with Panel of Normals and germline resource filte

NanoStat — Python tool for calculating statistics from Oxford Nanopore and PacBio long-read sequencing data. Reads FASTQ, FASTA, BAM, and sequencing summary files to produce read length distributions,

NanoSV — structural variant caller for long-read sequencing data (Oxford Nanopore). Detects deletions, insertions, inversions, duplications, and translocations from split-read alignments in BAM files.

NCBI Genome Workbench — desktop application for integrated genomic data visualization, sequence analysis, and annotation. Supports interactive browsing of GenBank/RefSeq entries, multiple sequence ali

Nextclade CLI — viral genome quality control, clade assignment, mutation calling, and phylogenetic placement for SARS-CoV-2, influenza (H3N2, H1N1, H5N1), RSV, mpox, and 100+ other pathogen datasets.

NextDenovo — string graph-based de novo assembler for long reads. Performs error correction (NextCorrect) then assembly (NextGraph) from PacBio CLR, PacBio HiFi, or Oxford Nanopore reads. Config-file

Novoalign — high-accuracy short-read sequence aligner for Illumina and MGI platforms using full Needleman-Wunsch algorithm with affine gap penalties. Maps single-end and paired-end reads up to 950bp o

Novocraft suite — short-read alignment and BAM sorting for DNA-seq and RNA-seq. novoalign maps Illumina, Ion Torrent, and 454 reads to indexed reference genomes with Smith-Waterman scoring for high-ac

NOVOPlasty is a seed-and-extend de novo assembler for short circular genomes including mitochondrial genomes, chloroplast/plastid genomes, and small viral circular sequences from Illumina whole-genome

Use when performing precision HLA class I typing from NGS data with OptiType. Covers read mapping to HLA reference with YARA, Integer Linear Programming allele calling at 4-digit resolution for HLA-A,

Panaroo — graph-based bacterial pan-genome analysis pipeline that corrects annotation errors. Takes GFF3 files from Prokka or Bakta, builds a population-level gene graph, and outputs core/accessory ge

Pangolin — Phylogenetic Assignment of Named Global Outbreak LINeages for SARS-CoV-2. Assigns Pango lineages to consensus genome sequences using UShER (phylogenetic placement) or pangoLEARN (ML classif

Pavian — interactive R/Shiny web application for metagenomics analysis and visualization. Reads classification reports from Kraken, Kraken2, Bracken, MetaPhlAn, DIAMOND+MEGAN, and Centrifuge to genera

Pfam — database of protein families with curated HMM profiles for domain annotation, functional classification, and evolutionary analysis. Search protein sequences against Pfam-A using HMMER's hmmscan

PGAP — NCBI Prokaryotic Genome Annotation Pipeline for comprehensive annotation of bacterial and archaeal genomes. Runs gene prediction (GeneMarkS-2+, tRNAscan-SE), functional annotation via HMM/BLAST

Use when working with phantompeakqualtools — phantompeakqualtools (spp)

phytools — R package for phylogenetic comparative biology and the study of trait evolution on phylogenies. Provides ancestral state reconstruction (continuous and discrete), stochastic character mappi

Pilon — automated genome assembly improvement and variant detection tool. Polishes draft assemblies by correcting SNPs, indels, and misassemblies using short-read alignments (BAM files). Fills gaps in

PinAPL-Py (Pooled In/out Screen Analysis Pipeline for Python) is a complete analysis pipeline for pooled CRISPR sgRNA screens. Handles raw FASTQ alignment to sgRNA libraries, read counting, normalizat

Use when analyzing plant images for phenotyping with PlantCV. Handles visible (RGB), near-infrared (NIR), fluorescence, thermal, and hyperspectral imaging workflows. Performs image segmentation, shape

PLINK 1.9/2 — high-performance command-line toolset for whole-genome association analysis, population stratification, identity-by-descent, linkage disequilibrium computation, and genotype data managem

Use when working with Polypolish — a short-read polishing tool for long-read genome assemblies. Corrects errors in ONT or PacBio draft assemblies using paired Illumina short reads aligned with BWA. Us

Porechop — adapter trimming and demultiplexing tool for Oxford Nanopore long-read sequencing data. Finds and removes adapters from read ends, splits chimeric reads containing internal adapters, and de

PRINSEQ++ — high-performance C++ tool for quality control and preprocessing of FASTQ sequencing reads. Filters and trims reads by quality score, length, GC content, sequence complexity (DUST/entropy),

ProteoWizard msconvert — command-line mass spectrometry data converter for proteomics workflows. Use when converting vendor RAW files (Thermo, AB SCIEX, Waters, Bruker, Agilent) to open formats (mzML,

Purge_dups — haplotypic duplication identification and removal tool for genome assemblies. Detects and removes overlapping haplotigs and heterozygous duplications from primary assemblies using read de

Purge Haplotigs — pipeline for curating heterozygous diploid genome assemblies by identifying and reassigning haplotigs (alternative haplotype contigs). Analyzes read-depth histograms to set coverage

Use when working with pybedtools — pybedtools — Python interface to BEDTools

PycoQC — Python tool for Oxford Nanopore sequencing QC that parses basecaller summary files (sequencing_summary.txt from Guppy, Dorado, or MinKNOW) and BAM alignment files to generate interactive HTML

Pyrodigal is a Python library binding to Prodigal for gene prediction in prokaryotic genomes and metagenomes. Provides in-memory ORF finding with SIMD-accelerated scoring, single-genome and metagenomi

Qualimap — platform-independent quality control tool for next-generation sequencing alignment data. Provides BAM QC (coverage, insert size, GC content, mapping quality), RNA-seq QC (gene body coverage

QUAST (Quality Assessment Tool for Genome Assemblies) — evaluate genome assembly quality using contiguity metrics including N50, L50, total length, largest contig, misassemblies, and mismatches. Suppo

Racon — ultrafast consensus module for raw de novo genome assembly of long uncorrected reads (PacBio CLR, Oxford Nanopore). Uses partial order alignment (POA) to polish draft assemblies from miniasm,

RagTag — reference-guided genome assembly scaffolding, misassembly correction, gap patching, and multi-scaffold merging toolkit. Successor to RaGOO. Supports minimap2, unimap, and nucmer aligners. Pro

REGENIE — whole-genome regression for biobank-scale GWAS. Two-step ridge regression with leave-one-chromosome-out (LOCO) predictions for efficient single-variant and gene-based association testing. Su

RepeatMasker — screens DNA sequences for interspersed repeats and low-complexity regions. Uses Tandem Repeats Finder and curated repeat libraries (Dfam, RepBase) to identify SINEs, LINEs, LTR elements