This repository contains various developmental versions of the RAIDER tool for de novo sequence identification, as well as as automated tests for the analysis RAIDER results.

RAIDER code:

• RAIDER_src: Source code for original RAIDER prototype.
• RAIDER_prescan: Source cod for a low-memory version of RAIDER.
• RAIDER_srv_v2: Adaptation of RAIDER to spaced seed searches.
• phRAIDER: Current invocation of phRAIDER.

Simulation code:

• chromosome_simulator.py:
  • Generates simulated chromosomes based on an order-k Markov chain estimated from a template organism genome.
  • Leaves transposable element sequences intact, while generating inter-TE sequences from the Markov chain.
• markov_gen.py: Libraries for working with k-th order Markov chains:

Pipeline code:

• redhawk.py: Python library for interfacing with a pbs job management system
• Raider_eval.py: Pipeline for automated comparison of de novo TE identification tools (deprecated)
• testing_pipeline.py: New pipeline for initiating large batches of TE identification tool runs in parallel on a PBS cluster
• collect_stats.py: Analysis scripts -- collect results from testing_pipeline.py output and create result tables.

Analysis code:

• analysis*.R: R code for generating plots and statistical analysis from the pipeline output

Authors:

• Nathanial Figueroa
  • Co-author: RAIDER
• Xiaolin Liu
• Carly Schaeffer
  • Co-author: phRAIDER
  • Contributed to developement of pipeline code.
• Dr. John Karro (Primary investigator)
  • co-author: RAIDER, RAIDER_eval
  • Primary developer of simulation code, pipeline code, analysis code