Feature comparison of long-read sequencing STR genotyping tools
| Feature | STRkit | LongTR | TRGT | Straglr | STRdust | Notes |
|---|---|---|---|---|---|---|
| Copy number output | ✓ | – | ✓ | ✓ | – | |
| Allele size confidence intervals | ✓ | – | ✓ | ✓ | – | |
| Allele consensus sequence output | ✓ | ✓ | ✓ | – | ✓ | Straglr v1.5.2+ VCFs use symbolic alternate alleles. |
| Beyond read-length genotyping | – | – | – | Partial | – | Straglr can use reads that cover only part of a repeat to support alleles, but it does not have a size model that incorporates in-repeat reads like some short-read STR genotypers. |
| De novo proximate SNV phasing | ✓ +output | – | ✓ | – | – | STRkit and TRGT can use heterozygous SNVs to cluster STR alleles; STRkit can output them to VCF. |
| Existing phased SNV incorporation | – | ✓✓ | – | – | – | |
| Haplotagged alignment file support | ✓ | ✓ | ✓ | – | ✓ | All but Straglr can use phased read data from, for example, WhatsHap (Martin et al. 2016), to call STRs. |
| Methylation handling | – | – | ✓✓ | – | – | |
| ONT read support | ✓ | ✓ | Explicitly forbidden | ✓ | ✓ | TRGT theoretically works on ONT data but is forbidden by the software license. |
| Read-level data | ✓ | – | Partial | ✓ | ✓ | STRkit: JSON output with read-level peak ID+sequence data; TRGT: overlapping reads in BAM; Straglr: TSV output with read-level copy numbers; STRdust: read-level sequence output in VCF. |
| Mendelian inheritance calculation tool | ✓✓ | – | – | – | – | STRkit includes a tool to output loci that do not respect Mendelian inheritance in a set of trio VCFs. |
| Free and open-source software license | Yes (GPLv3) | Yes (GPLv2) | – | Yes (GPLv3) | Yes (MIT) | TRGT's license restricts it to be only used with PacBio sequencing data, and the software cannot be forked and subsequently redistributed. |
| Multithreading/processing | ✓ | – | ✓ | ✓ | ✓ |
[i] Comparison of features of STRkit with those of recent long-read sequencing STR genotyping tools: LongTR, TRGT, Straglr, and STRdust. Features with double check marks are unique to that particular tool.