HaploGrep2 publication

Happy to announce the publication of the HaploGrep2 paper in this years Web Server Issue 2016 in Nucleic Acids Research. For data generated with massive parallel sequencing devices in form of fastq or bam files, the mtDNA-Server paper also published in this years issue, gives some details there.

 

1000G Phase 3 mtDNA data available

The 1000 Genome Consortium recently released the Phase 3 mitochondrial DNA data of over 2,500 samples for download, besides their papers in Nature, stating: Mitochondrial chromosome variants are now available for the Phase 3 individuals from our FTP site Since in the current Version HaploGrep 2 can deal with the VCF file (unzipped), all 2500 … 

 

NGS, HaploGrep and Hadoop MapReduce

Many of our HaploGrep users are interested in analysing data within automated pipelines. To support users with a scalable and standardized service, we are happy to present you our newest project, called mtDNA-Server. mtDNA-Server provides a free service for the complete workflow of NGS mtDNA projects. It includes the alignment of FASTQ SE/PE data based … 

 

Importing VCF file to HaploGrep 2.0

With the establishment of NGS-Devices and the resulting data flood, new file formats such as FASTQ, SAM, BAM or VCF became de-facto standards in the bioinformatics data world. Especially the VCF-file containing the variants became of special interest in the user requests lately.¬†There are some python scripts available, that convert a VCF file to a … 

 

rCRS vs. RSRS vs. HG19 (Yoruba)

It’s not always straight forward when¬†working with the human mitochondrial DNA, even if it comes to the question: “what reference sequence do you use?” There should be just one reference and the questions therefore obsolete – what however is not the case. Since the first sequencing of the human mitochondrial genome by Anderson et al. …