This tool is replaced by BAM Analysis Kit with more advanced features.
A telomere is a region of repetitive nucleotide sequences at each end of a chromatid, which protects the end of the chromosome from deterioration or from fusion with neighbouring chromosomes. The longer the telomere, the more long life you have.
I did a small experiment to see if I could extract the telomere length information from BigY BAM and indeed I was able to. So, I made a small tool using telseq on windows using cygwin so that anyone can use it.
The tool provides the following output,
- telomere.txt - Information on telomere length.
- Big-Y BAM
- Any BAM file with UCSC convention (hg1x) ordering for human reference genome.
- Windows 64 bit Operating System
- Microsoft .Net Framework 4.0
- 2 GB of free hard disk space.
- Minimum 2 GB RAM.
Extract the download and click 'BigY Telomere UI'. Select the .BAM file and click 'Start Analysis'.
After clicking 'Start Analysis', a command prompt will automatically open and start executing a few commands.
After a few minutes (depending on your computer speed), the output will be available inside a subfolder called 'out', and the result file will automatically open in notepad. The estimated telomere length is in kb.
License: The download bundles the following software for easy usage.
- Ding, Zhihao, Massimo Mangino, Abraham Aviv, Tim Spector, and Richard Durbin. "Estimating telomere length from whole genome sequence data." Nucleic acids research (2014): gku181.
- Some modifications for compatibility.
- Initial Release.