TELR v1.1

• update readme
• add citation file
• fix off-by-on error in TSD module
• fix repeatmasker sorting error
• fix long filename issue

TELR v1.0

• Update README.
• Official release of TELR.
• This revision is used in the following manuscript.

Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line
Shunhua Han, Guilherme B. Dias, Preston J. Basting, Raghuvir Viswanatha, Norbert Perrimon, Casey M. Bergman (2022) Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line Nucleic Acids Research 50:e124 https://academic.oup.com/nar/article/50/21/e124/6717830

TELR v0.2

• Add module to estimate intra sample TE allele frequency.
• Update algorithm to predict TE insertion coordinate.
• Expand flexibility to choose alignment method, local contig assembly method and contig polishing method.
• Report final predictions in VCF, JSON, and BED format.
• TELR repo is now pip installable.

TELR v0.1

This version of TELR shows good performance on several real drosophila melanogaster data sets.