Table 2. The list of available bioinformatics tools for mtDNA analysis.
| MitoSuite | HaploGrep2 | mtDNA-Server | mtDNAprofiler | MToolBOX | MitoSeek | |
|---|---|---|---|---|---|---|
| Input file | BAM | FASTA, hsd, VCF | FastQ, BAM, VCF | FASTA, varianta | FastQ, BAM, SAM | BAM |
| User interface | GUI | Web | Web | Web | CUI | CUI |
| Supported reference sequence | rCRS, RSRS, hg19c, GRChc | rCRS, RSRS | rCRS, RSRS | rCRS | rCRS, RSRS | rCRS, hg19c |
| Automatic installation | ✓ | – | – | – | – | – |
| File upload | – | ✓ | ✓ | ✓ | – | – |
| Haplogroup assignment | ✓ | ✓ | ✓ | – | ✓ | – |
| mtGenome assembly | ✓ | – | ✓ | ✓ | ✓ | ✓ |
| Coverage plot | ✓ | – | ✓ | – | – | – |
| Quality check | ✓ | – | ✓ | – | – | ✓ |
| Concordance check | ✓ | – | – | ✓ | – | – |
| Damage check | ✓ | – | – | – | – | – |
| Contamination check | ✓ | – | ✓ | – | – | – |
| Relative copy number | – | – | – | – | – | ✓ |
| Variant annotation | ✓ | – | ✓ | – | ✓ | ✓ |
| Structural variants detection | – | – | – | – | – | ✓ |
| Somatic mutation detection | – | – | – | – | – | ✓ |
| Heteroplasmy detection | ✓ | – | ✓ | – | ✓ | ✓ |
Notes.
- ✓
- available
- –
- not-available
a
A text-based format for describing SNPs information against a reference seuquence.
b
A text-based format for describing the base-pair information of the reads against a reference sequence.
c
Support for the mitochondrial sequence (chrM/chrMT) on hg19, GRCh37 and 38.