G_agassizii_reference_update

This repository contains scripts used in processing and updating the Gopherus agassizii reference genome to version 1.1

There are two Python scripts, Remove_and_split_contamination.py and Trim_Ns_fasta.py. Both require Python 2.7 because of the iteration syntax on lines 61-65 in Remove_and_split_contamination.py and lines 86-88 in Trim_Ns_fasta.py. In both cases, manually changing .next() to ._next_() should make the scripts Python 3 compatible.

For more details on how we used the scripts in our update to the G. agassizii reference, see our preprint:

Webster TH, Dolby GA, Wilson Sayres MA, Kusumi K. (2018) Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1. PeerJ Preprints 6:e3266v4. https://doi.org/10.7287/peerj.preprints.3266v4

If you use these scripts, please cite this paper. And if you run into any problems or have any questions, please open an Issue in our Github repo

The assembly is available at NCBI and the assembly and annotation are available on Harvard's Dataverse.

Tim Webster - Updated Jan 31, 2018