Table 1 Comparison of the features, algorithms and input formats of common software used to detect mobilization of TE and/or structural variations
From: TE-Tracker: systematic identification of transposition events through whole-genome resequencing
Software | Type | Input data and format | discordant reads detection | transposition calling | Every potential mapping considered | Detection of unknow TEs insertion | Precision | Donor/Acceptor output |
|---|---|---|---|---|---|---|---|---|
TE-Tracker | BAM file | ✓ | ✓ | ✓ | ✓ | 100 bp-1 Kbp | ✓ | |
RetroSeq | TE-dedicated | BAM file, TE annotation or sequence | ✓ | ✓ | ✗ | ✗ | 100 bp-1 Kbp | ✓ |
Tea | TE-dedicated | BAM file, TE annotation or sequence | ✗ | ✓ | ✗ | ✗ | 1 bp | ✓ |
T-lex | TE-dedicated | FASTQ file, TE annotation | ✗ | ✓ | ✗ | ✗ | 1 bp | ✓ |
Popoolation-TE | TE-dedicated | FASTQ file, TE sequence and TSD annotation | ✗ | ✓ | ✗ | ✗ | 1 bp | ✓ |
TE-locate | TE-dedicated | FASTQ file, TE sequence | ✗ | ✓ | ✗ | ✗ | 1 bp | ✓ |
ngs_te_mapper | TE-dedicated | FASTQ file, TE annotation | ✗ | ✓ | ✓ | ✗ | 1 bp | ✗ |
RelocatTE | TE-dedicated | FASTQ file, TE sequence | ✗ | ✓ | ✓ | ✗ | 1 bp | ✓ |
TIF | TE-dedicated | FASTQ file, TE sequence and TSD annotation | ✗ | ✓ | ✗ | ✗ | 1 bp | ✓ |
VariationHunter | SV | DIVET alignment file (mrFAST output) | ✗ | ✗ | ✓ | ✓ | 100 bp-1 Kbp | ✓ |
PRISM | SV | BAM file | ✓ | ✗ | ✗ | ✓ | 1 bp | ✗ |
Delly | SV | BAM file | ✓ | ✗ | ✗ | ✓ | 1 bp | ✗ |
GASVpro | SV | Alignment file and coverage data file | ✓ | ✗ | ✓ | ✓ | 100-1 kp | ✗ |
Hydra | SV | Discordant reads coordinates and mapping features | ✗ | ✗ | ✓ | ✓ | 1 bp | ✗ |