BAM/CRAM to T2T Alignment

T2T-CHM13 is the first truly complete human genome reference, covering all chromosomes from telomere to telomere without gaps. Unlike GRCh38, which has approximately 151 Mb of missing sequence, T2T-CHM13 provides complete coverage including centromeric regions, acrocentric chromosome arms, and other previously unresolved areas. This enables more accurate alignment and analysis in regions that were previously inaccessible.

Yes. We accept BAM or CRAM files previously aligned to any common reference genome build (hg19/GRCh37 or hg38/GRCh38), indexed or unindexed. The original reads are extracted and then re-aligned from scratch to the T2T-CHM13 reference using the optimal algorithm for your read type.

Upload your file to a file-sharing service such as Google Drive or Dropbox, create a sharing link that allows downloading, and paste the link during the order. Whole genome files are large (often 30 GB or more), so please make sure the upload is complete before sharing the link. Once we confirm that the download is complete, you can remove the shared file from your storage.

Processing typically takes 24-48 hours from when we have downloaded your file, depending on file size and current queue. Whole genome sequencing files at 30x coverage usually complete within about 48 hours. We'll notify you via email when your results are ready for download.

You will receive a coordinate-sorted BAM file aligned to T2T-CHM13, along with its index file (.bai). We also provide alignment statistics including mapping rate, coverage distribution, insert size metrics (for paired-end data), and quality score distributions. All files are delivered via secure download link.

No. This service delivers the re-aligned BAM, its index and the alignment statistics. Variant calling is not part of this package. Our RAW to VCF and VCF Annotation services work from RAW and VCF files and do not call variants from a BAM or CRAM file.

This service is intended for research and ancestry purposes only. It is not designed, validated, or certified for clinical diagnostics, medical decision-making, or health-related interpretations. For clinical applications, please consult with appropriate certified laboratories and healthcare providers.