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Human Genome Reference FASTA Files

Resource Location

/labs/SysMedBio/Q/Resources/Genomics/Fasta

/Volumes/lab/SysMedBio/Resources/Genomics/Fasta

Q:\SysMedBio\Resources\Genomics\Fasta

This resource contains standard human genome reference sequences in FASTA format, along with index and coordinate compatibility files.

Scientific Context

Reference genomes serve as a standardized coordinate system and digital map of a species' genome (in this case, Homo sapiens). Rather than representing a single individual, the reference is a mosaic constructed from the DNA of multiple anonymous donors, providing a baseline map to align and compare newly sequenced genomic reads.

Reference Genomes: hg19 vs. hg38

  • hg19 (GRCh37): Released in 2009 by the Genome Reference Consortium (GRC). It served as the primary standard for more than a decade and remains widely used in clinical diagnostics due to historical databases, clinical pipelines, and annotation dependencies.
  • hg38 (GRCh38): Released in 2013, this is the current recommended reference assembly. It corrected thousands of structural and sequence-level assembly errors from hg19, closed sequence gaps, updated centromeric regions, and introduced alternative loci (ALT contigs) to better represent human genetic diversity.
  • Coordinate Conversion: Because of structural corrections and gaps closed in hg38, genomic coordinates differ between hg19 and hg38. Alignments or variant coordinates cannot be directly compared without a coordinate translation tool (e.g., LiftOver).

Accessory Files

  • FASTA Index (.fai files): Because human genome reference files are very large (approx. 3 GB), index files are generated (using tools like samtools faidx). The index maps the byte offset of each sequence/chromosome in the FASTA file, enabling bioinformatics software to perform rapid, random access to specific regions without reading the entire file into memory.
  • Chromosome Name Mappings (synonyms.txt): Different bioinformatics databases use different naming conventions for chromosomes. For example, Ensembl and NCBI style identifiers are integers (1, 2, X, MT), whereas UCSC style identifiers prefix these with "chr" (chr1, chr2, chrX, chrM). Synonym files map these names to ensure compatibility across different tools and databases.

Available Files

The following files are available in the Fasta resource directory:

  • synonyms.txt: A translation table mapping Ensembl/NCBI style chromosome names to UCSC style names to ensure compatibility.
  • hg19/hg19.fa: The FASTA reference sequence for the human genome assembly version hg19 (GRCh37).
  • hg19/hg19.fa.fai: The samtools-generated index file for the hg19 reference.
  • hg38/hg38.fa: The FASTA reference sequence for the human genome assembly version hg38 (GRCh38).
  • hg38/hg38.fa.fai: The samtools-generated index file for the hg38 reference.