Table 1.
Comparison of different tools for analyzing TE abundance. The required input, the resulting output, notable features and shortcomings are shown for each tool (RepeatMasker [Smit et al., 1996‐2010] RepeatExplorer [Novák et al., 2013], dnaPipeTE [Goubert et al., 2015], RepLong [Guo et al., 2017] and DeviaTE)
| DeviaTE | RepeatMasker | RepeatExplorer | dnaPipeTE | RepLong | |
|---|---|---|---|---|---|
| Method | Alignment of reads to TEs | Alignment of TEs to assembly | De novo assembly | De novo assembly | De novo assembly |
| Input | Sequencing reads, TE sequences | Genome assembly, TE sequences | Sequencing reads, TE sequences | Sequencing reads (single‐end only), TE sequences, genome size estimate | Sequencing reads, genome size estimate |
| Output | Variation within TE families, visualization of TEs, quantification of variation, estimates of TE abundance | Annotation of repeats, masked query sequence, genome proportion of repeat orders, divergence to consensus | TE contigs, genome proportion of TEs, abundance of contigs | TE contigs, genome proportions of TEs, estimates of relative age of TEs, abundance of contigs | TE contigs |
| Notable features | Divergence at nucleotide resolution, short and long reads, detects structural variants of TEs, container‐type installation, read preprocessing | Identify low complexity DNA, detect contamination in assembly, different search engines | Platform independent Galaxy server, read preprocessing, protein domain search, identification of novel repeats, suitable for low‐coverage sequencing | Identification of novel repeats, suitable for low‐coverage sequencing | Supports long‐reads, sensitive algorithm, suitable for low‐coverage sequencing, no TE library required |
| Shortcomings | No genomic position of TEs, no novel repeats | No quantification of families, no novel repeats, susceptible to low assembly quality | No genomic position of TEs, long runtimes | Installation requires RepBase subscription, no genomic position of TEs, no direct quantification of families | No quantification of families, does not consider sequencing quality, no genomic position of TEs |
| Availability (Win/Mac/Linux) | −/+/+ | −/+/+ | +/+/+ | −/−/+ | −/−/+ |