Software and Resources

https://github.com/asfistonlavie

• Drosophila melanogaster de novo genome assembly with TruSeq synthetic long-reads (McCoy et al., PLoS One 2014)
  • Raw synthetic long and short reads used in this study
  • GitHub repository of the scripts used for the genome assembly assesment developed by Rajiv McCoy

• Recombination rate estimation along the Drosophila melanogaster chromosomes (Fiston-Lavier et al., Gene 2009)
  • Drosophila Recombination Rate Calculator (RRC)

• Repeat annotation
  • Transposable elements
    • Transposable element discovery and annotation: T-lex2 (Fiston-Lavier et al., NAR, 2011, 2014)
    • Transposable element population frequencies in Drosophila melanogaster data
  • Segmental duplications
    • Segmental duplication annotation: REPET – SegDup (Fiston-Lavier et al., Genome Research 2007) Segmental duplication annotation in Drosophila melanogaster genome
  • Tandem repeats
    • Tandem repeat annotation and analysis: REPET – SATannot