Over the last years, HaploGrep became the de facto standard for automatic haplogroup classification (~ 18.000 users, cited over 140 times, about 120 local installations) and is also used in several commercial systems and research pipelines. There was quite some work done underneath the surface of HaploGrep, especially to improve our haplogroup classification performance and to keep up with the latest requirements. After almost a year in beta (see entry from Sept 2014), we think it’s finally time to replace the initial version of HaploGrep with the new and improved version Haplogrep2. We hope you like the new version and would appreciate any kind of feedback!
These are the major improvements:
- Improved classification algorithm resulting in a speed up of 20x!
- HaploGrep includes now a rule-based engine. The two new columns “warnings” (W) and “errors” (E) are showing abnormalities in the input file detected with the new engine. We very much appreciate the input and suggestions from Hans Bandelt and Antonio Salas!
- New Import Formats (VCF + FASTA) supported
- Updated to the latest security standards on server side. So we are finally back on Firefox!
- Apply different ranking algorithms (e.g. Jaccard, Hamming Distance) besides our default ranking algorithm, the Kulczynski distance. These new ranking algorithms will be introduced one by one and are therefore currently disabled.
- Provide HaploGrep also as a command line version (included in mtDNA-Server)
- Direct support of VCF files through the Htsjdk library.
New export formats supported:
- VCF (currently without deletions)
- Fasta sequences
- Multiple Alignment Sequences in Fasta format
- Phylogenetic Tree for publication ready plots
- The haplogroups extended format reports the information of the remaining and expected polymorphism for the best hit haplogroup
Points we (currently) removed from the beta:
- Removed direct support of heteroplasmic sites (Y,R)
- How to use the REST-API.
- Fasta Import is available (open a *.fasta file!) but still in beta.
Here’s the updated version: HaploGrep2