Hite

Bug fix
1. Remove unnecessary parameters.
2. Resolved some user input and output issues.
3. Resolved the issue with incomplete classification.

Improvements
1. By re-aligning the candidates to the genome, we remove single-copy TIR elements, which reduces the number of false positives.

Summary of functions and features

1. Remove the RepeatMasking module, which saves a lot of pairwise alignment time (Oryza sativa: 3.44 h -> 0.98 h) and slightly increases the number of Perfect TE models (Oryza sativa: 847 -> 892).
2. Provide conda one-step installation.
3. Remove RepeatClassifier from HiTE and add RepeatModeler to provide RepeatClassifier function.
4. Remove temp files and directories if not in debug mode.

Summary of functions and features

HiTE has undergone extensive benchmarking and has proven to be the best TE annotation tool available.

1. Discover and annotate high-precision structurally intact TEs, including LTR, TIR, Helitron, LINE, and SINE elements.
2. Reduce false positives and unwrap nested TEs.
3. Automatic checkpointing, so that HiTE can automatically restart from where it was interrupted.