Track by Sequence fragments

CR or HVRs, and then coding regions

Track by complete mtGenome seq.

 

Track by Variant profiles

Fragments ~ complete mtGenome


Haplotracker

"Simple and accurate mtDNA haplogrouping application"

A web application for mitochondrial haplogrouping from fragmented DNA: Highly accurate prediction using small fragmented control-region (CR) sequences, simple tracking for confirmation or sub-haplogrouping by narrowing and differentiating highly-ranked haplogroups, and conserved region mapping for successful primer design.

Haplotracker is a mtDNA haplogroup (HG) tracking application specifically designed for fragmented DNA samples, such as degraded DNA, commonly found in forensic specimens or human remains and difficult to obtain large DNA sequences.

Haplotracker predicts highly probable HGs first with CR sequence fragments. It then narrows down the HGs and differentiate between them for simple tracking of HG-confirmation and sub-haplogrouping.
DOI: 10.1101/2020.04.23.057646


High Accuracy using Control-region sequences

Highly accurate prediction of HG using CR or HV region sequence fragments.

  • Using a novel algorithm based on PhyloTree definitions and our scoring system built with big data of haplotypes (n=118,869)
  • Extensively evaluated with 54,538 CR sequence samples comparing with other servers

A novel HG-tracking solution

It was established through repeated blind simulation tests

  • Inputs sequence fragments via a unique user-friendly interface
  • Minimizes the number of tests for HG tracking by narrowing down the predicted HGs by the integration of HGs to their MRCAs
  • Proposes differential variants between HGs
  • Re-tracks with the fragments of proposed variants to confirm the HGs or to track sub-haplogroups

Additional tools

  • 'HG tracking by fragment variant profiles' for variant profile input instead of sequences once the sample fragments are sequenced and their variants are extracted using the main tool.
  • 'Conserved region mapping tool for primer design' to secure successful PCR that is necessary to obtain additional sequences for further tracking.
  • 'HG database' to explore Phylotree HGs and their sub-haplogroups with their defining variant profiles.
  • 'Differntiation between HGs' to find differential variant information among user-inputted HGs.
  • QC tools: analysis of potential artificial recombination (included in main tools) and potential phantom mutants in a dataset
  • Variant format conversion tool for Phlyotreee, MitoTool, HaploGrep 2, and EMPOP
  • Haplogrouping by complete mtGenome sequence
  • Major HG-specific variants

Super-HG prediction rates with CR sequences

Super-HG prediction rates


References

References