Table 2. Software dependencies required to install and run each component TE detection method in the McClintock pipeline.
| Software | ngs_te_mapper | RelocaTE | TEMP | RetroSeq | PoPoolationTE | TE-locate | Version Used in this Study |
|---|---|---|---|---|---|---|---|
| Linux | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | CentOS 6 |
| Perl | ✓ | ✓ | ✓ | ✓ | ✓ | 5.18.1 | |
| R (R Core Team 2013) | ✓ | 3.0.2 | |||||
| BioPerl (Stajich et al. 2002) | ✓ | ✓ | 1.006001 | ||||
| RepeatMasker (Smit et al. 2013) | ✓ | 4.0.2 | |||||
| BEDTools (Quinlan and Hall 2010) | ✓ | ✓ | 2.17.0 | ||||
| SAMTools (Li et al. 2009) | ✓ | ✓a | ✓ | ✓ | 0.1.19-44428cd | ||
| BCFTools (Li et al. 2009) | ✓ | 0.1.19-44428cd | |||||
| twoBitToFa (Kuhn et al. 2013) | ✓ | 294 | |||||
| BLAT (Kent 2002) | ✓ | 35 × 1 | |||||
| Exonerate (Slater and Birney 2005) | ✓ | 2.2.0 | |||||
| Bowtie (Langmead et al. 2009) | ✓ | 1.0.0 | |||||
| BWA (Li 2013) | ✓ | ✓ | ✓ | ✓ | ✓ | 0.7.4-r385b |
a
Only compatible with SAMTools 0.1.19 or earlier (Rishishwar et al. 2016).
b
This specific version of BWA is needed to ensure compatibility between PoPoolationTE, which uses BWA-ALN, and other component methods which use BWA-MEM.