RRC  I designed the Drosophila Recombination Rate Calculator (RRC) which is a web-based tool to estimate the rates of recombination anywhere in the D. melanogaster genome. The RRC is fast, and is tailored to specific requests such as the genome or annotation release (Fiston-Lavier et al. 2010 Gene).
 I designed the T-lex package that is a computational tool to annotate individual transposable element (TE) insertions in strains
or population using next-generation sequencing (NGS) data. The original version of the T-lex
pipeline has been published (Fiston-Lavier et al. 2011 NAR).
This version included a pipeline to call the presence and/or absence of
individual annotated TE insertions. I redesigned this pipeline to
handle paired-end data of individual and pooled sample. The new version
of the T-lex presence/absence pipeline is available at http://petrov.stanford.edu/cgi-bin/Tlex.html. T-lex2 is now composed of two pipelines. Both pipelines combine single or paired-end read mapping with
the read depth coverage information and handle individual or pooled sample.  (A) The
“presence/absence” pipeline can be used to call individual TE insertions annotated in a reference sequence by determining their presence and/or absence in strains sequenced. This pipeline can be also used to annotate
the TSD (Target Site Duplication) of individual TE insertions.
Combining calls from several strains from a same population, the
"presence/absence" pipeline can estimate the population frequency of
each TE insertion. (B) The “de novo” pipeline can be used to discover and annotate TE insertions not annotated in the reference sequence. T-lex is in active development with the help of the T-lex team (contact afiston [at] stanford [dot] edu). T-lex TEAM: - Anna-Sophie Fiston-Lavier, My students: - Maite Barron - PhD student, - Barrientos Mauricio - master student, - Vippala Lokitha - master student, - Dave Tushar - master student, - Matthew Carrigan - undergraduate student. - Dmitri Petrov - Professor @ Stanford University, - Josefa Gonzalez - Group leader @ Institute of Evolutionary Biology, - Aleksandr Arhipov - admin system @ ScaleGenomics. |