Table 1.
Tools selected for the benchmark of TE insertions
| Tool | Target | Prediction | Input | Output format | Perceived difficulty | Manual | |
|---|---|---|---|---|---|---|---|
| Installation | Input preparation | ||||||
| RelocaTE2 | Non-reference insertions | All families | fastq | gff file | Easy | Easy | https://github.com/JinfengChen/RelocaTE2 |
| Jitterbug | Non-reference insertions | All families | Bam | gff file | Medium | Medium | https://github.com/elzbth/jitterbug |
| Retroseq a | Non-reference insertions | All families | Bam | vcf file | Easy | Difficult | https://github.com/tk2/RetroSeq/wiki/RetroSeq-Tutorial |
| ITIS | Non-reference insertions | Single-family | fastq | Bed file | Easy | Medium | https://github.com/Chuan-Jiang/ITIS |
| MELT | Reference and non-reference insertion | Single-family | Bam | vcf file | Easy | Medium | http://melt.igs.umaryland.edu/manual.php |
| PopoolationTE2 | Reference and non-reference insertions | All families | fastq | Tool-specific | Easy | Easy | https://sourceforge.net/projects/popoolation-te2/ |
| Teflon | Reference and non-reference insertions | All families | fastq | Tool-specific | Medium | Medium | https://github.com/jradrion/TEFLoN |
| Trackposon | Reference and non-reference insertions | Single-family | fastq | Bed file | Easy | Easy | http://gamay.univ-perp.fr/~Panaudlab/TRACKPOSON.tar.gz |
| TEMP a | Reference and non-reference insertions | All families | Bam | Tool-specific | Easy | Difficult | https://github.com/JialiUMassWengLab/TEMP/blob/master/Manual |
| TE-locate a | Reference and non-reference insertions | All families | Sam | Tool-specific | Easy | Difficult | https://sourceforge.net/projects/te-locate/ |
| PopoolationTE a | Reference and non-reference insertions | All families | fastq | Tool-specific | Easy | Difficult | https://sourceforge.net/p/popoolationte/wiki/Workflow/ |
| ngs_te_mapper a | Reference and non-reference insertions | All families | fastq | Bed file | Easy | Difficult | https://github.com/bergmanlab/ngs_te_mapper |
| McClintock | Reference and non-reference insertion | All families | fastq | Bed file | Easy | Difficult | https://github.com/bergmanlab/mcclintock |
a These tools were run as part of the McClintock pipeline. Perceived difficulty refers to McClintock and not the original methods
Installation: Easy = available in Conda, or automatic / semi-automatic installation. Medium = Needs several dependencies or specific versions of packages that need manual installation. Input preparation: Easy = can be run using common formats (ie fasta, bed) without the need of specific formatting. Medium = Needs specific formatting. Difficult = Needs very specific formatting