🌐 Reference Genomes Atlas 100 Curated Landmark Organisms ⚡ Live Search Across 100,000+ NCBI Sequenced Genomes 20 Sequencing File Formats

Reference Genomes Atlas

Authoritative reference directory of sequenced biological life forms across all major branches of life—from complete human assemblies (GRCh38.p14, T2T-CHM13) and model mammals to crops, yeasts, extremophilic archaea, and viral pathogens. Browse 100 curated landmark reference organisms below or search any of the 100,000+ sequenced genomes in the global NCBI Datasets repository in real time.

100 Curated Landmark Reference Genomes

100,000+ Searchable NCBI / Ensembl Species

8 Phylogenetic Branches

20 Sequencing File Formats

🔬 Select or Search Any Sequenced Organism

Sample: Homo sapiens (Human) active

Select from 100 Curated Reference Species:

Or Search Any Species on Earth (NCBI Datasets / RefSeq):

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Filter by Taxonomic Group:

Quick Models:

Mammalia (Primates & Mammals) NCBI TaxID: 9606 ★ Featured Sample Reference

Homo sapiens

• Human

Eukaryota Metazoa Chordata Mammalia Primates Hominidae Homo H. sapiens

Genome Size 3.10 Gb

Coding Genes 20,440

Total Genes 63,494

GC Content 41.0%

Karyotype / Topology 23 pairs (2n = 46)

Latest Reference 2023 (Ensembl 113 / GENCODE v46 / RefSeq GCF_000001405.40)

GRCh38.p14 / T2T-CHM13v2.0

🧬 Genome FASTA 📜 cDNA / CDS 🏷️ GTF 📑 GFF3 🥩 Protein 🌐 NCBI 🔭 UCSC

Legacy Standard 2009 (Ensembl 75 / GENCODE 19 / NCBI GCF_000001405.13)

GRCh37 / hg19 (Still used widely in clinical panels)

🧬 Legacy FASTA 📜 Legacy cDNA 🏷️ Legacy GTF

High-Throughput Sequencing File Formats & Coordinate Standards

Next-generation sequencing (NGS), long-read third-generation sequencing (PacBio HiFi, Oxford Nanopore), and single-cell omics rely on strictly standardized file specifications. Understand the exact coordinate conventions (0-based half-open vs. 1-based closed), mandatory headers, and companion index files across all pipeline stages.

Raw Sequencing Reads .fastq / .fq.gz

FASTQ (Fast Quality)

The de facto standard for raw high-throughput nucleotide sequencing reads. Stores 4 lines per read: @header, sequence, '+' delimiter, and ASCII-encoded Phred quality scores (Q = -10 * log10(P_error)).

Coordinates: N/A (Sequence + Quality)

Index: bgzip + fqidx (optional)

Tools: fastp, FastQC, Trimmomatic, Seqtk, Cutadapt

🔬 Select or Search Any Sequenced Organism

Homo sapiens

High-Throughput Sequencing File Formats & Coordinate Standards

FASTQ (Fast Quality)

SRA (Sequence Read Archive)

POD5 / FAST5 (Nanopore Raw Signal)

Unmapped BAM (uBAM / CCS)

FASTA (Genomic / Nucleotide)

2bit (UCSC Packed Nucleotide)

AGP (Assembly Golden Path)

SAM (Sequence Alignment/Map)

BAM (Binary Alignment/Map)

CRAM (Compressed Reference Alignment)

GTF 2.2 (Gene Transfer Format)

GFF3 (Generic Feature Format v3)

BED (Browser Extensible Data)

bigWig (Binary Continuous Signal Track)

VCF 4.2/4.3 (Variant Call Format)

BCF (Binary Variant Call Format)

GVCF (Genomic VCF)

MEX (Matrix Market Sparse Format)

H5AD (AnnData HDF5)

mmCIF / PDB (Macromolecular Structure)

⚡ Automated CLI Download Snippet