Error-prone human genomic sequence data from Illumina sequencing platform

Question

[rbpdee]

I am curious if there is any publicly available bed or other forms of track showing sequencing error-prone sequences or regions in the human genome. To be precise, I am looking for DNA regions that often tend to show insertions or deletions due to sequencing errors from DNA pol slippage, e.g, stretches of As or Gs (homopolymeric regions).

Alternatively, a list of sequences that are difficult to sequence with the Illumina Sequencing platform could work too!

rbpdee

Answer 1

[donfreed]

You might try the GA4GH genome stratifications, https://github.com/genome-in-a-bottle/genome-stratifications

The resource includes many regions (as BED files) that are difficult to sequence with short-read technology (low-mappability, low-complexity, etc.). In particular, the homopolymer and simple repeat regions in the LowComplexity folder will be enriched for "sequencing errors from DNA pol slippage".

[rbpdee]

Thanks donfreed! I will look into it.