The ambitious challenge of finishing the human genome

The current human reference genome assembly, known as Genome Reference Consortium Human Build 38 (GRCh38 or hg38), does not contain a complete sequence of the human genome. The missing portions of the genome mostly lie in heterochromatic regions and near the centromeres and telomeres, and their sequences were never determined due to difficulties in mapping, cloning, or assembling the reads. Though absent from the reference, these sequences are known to contain genes and other functional elements that may be relevant to human health and disease.

The first complete telomere-to-telomere sequence of a human chromosome, the X chromosome, was published in July 2020. Using new sequencing technologies from PacBio and Oxford Nanopore, researchers were able to generate high-coverage, ultra-long reads that span hundreds of thousands of base pairs which helped bypass some of the challenges of the chromosome sequence assembly.

The new X chromosome sequence comes from the CHM13 (complete hydatidiform mole) cell line which is uniformly homozygous and has a 46,XX karyotype. This effectively haploid genome was used to avoid having to assemble both haplotypes of a "normal" diploid genome.

The X chromosome is linked to a number of diseases such as haemophilia, chronic granulomatous disease, and Duchenne muscular dystrophy. Closing the gaps in the X chromosome sequence assembly marks an important milestone in genomics and medical genetics.

See also

• Genome Browser - Explore the human genome.
• Sequence Logo Generator - Create sequence logos from FASTA alignments.
• WebLogo in the browser - Bringing WebLogo to the browser + demo of a pure client side sequence logo maker.
• BLAST WASM - Compiling the BLAST sequence search/alignment tool to WASM.
• DESeq2 in the browser - Running DESeq2 in the browser.
• Sequence Alignment Viewer - Open FASTA files in the browser.
• Phylogenetic Tree Editor - An online visual editor for phylogenetic trees (WIP).
• Phylogenetic Tree Builder - Reconstruct phylogenetic trees from protein or DNA/RNA sequence alignments.
• Plasmid Map Generator - A tool to generate plasmid maps from GenBank files.
• WikiPathways: A Wikipedia for biological pathways - An overview of the collaboratively edited structured pathway encyclopedia.
• The RDF model of the Gene Ontology, demystified - An outline of the structure of the Gene Ontology RDF graph and ways to query it.
• Scalable genomic alignment with Progressive Cactus - How progressive alignment makes it possible to efficiently align hundreds to thousands of large genomes.
• GenBank to FASTA - Convert GenBank flat files to FASTA format.
• ABI to FASTA - Convert AB1 files (Applied Biosystems/ABI trace files) to FASTA format.
• Awesome bioinformatics - A curated list of awesome resources on bioinformatics.
• NCBI Taxonomy Browser - A simple tool for viewing the NCBI taxonomy tree.
• What is FASTA and how is it used? - Learn about the FASTA format and its applications.
• FASTA Editor - A FASTA editor for creating and editing FASTA files.
• FASTA Parse Tree Viewer - Visualize the parse tree of FASTA files.
• FASTQ to FASTA Converter - Convert FASTQ files to FASTA format.
• FASTQ Editor - A FASTQ editor for creating and editing FASTQ files.
• Newick Editor - An online editor for phylogenetic trees in the Newick format.
• Newick Parse Tree Viewer - View the parse trees of Newick strings.
• PDB Editor - Edit PDB files online.
• PDB to FASTA - Extract protein/nucleotide sequences from PDB files.
• Bioinformatics Crossword - A daily crossword puzzle for bioinformatics terms.
• Bioinformatics pronunciation guide - A pronunciation guide for bioinformatics terms.