Benchmarking BleTIES with simulated reads from Paramecium

Source data and setup

This repository supplements our preprint describing the BleTIES software.

MAC and MAC+IES assemblies (both v1) from Paramecium tetraurelia strain 51, obtained from ParameciumDB

Download and install the following software in the opt/ folder:

ART read simulator https://www.niehs.nih.gov/research/resources/assets/docs/artbinmountrainier2016.06.05linux64.tgz
PBSIM read simulator (v2): git clone [email protected]:yukiteruono/pbsim2.git
minimap2 mapper: git clone https://github.com/lh3/minimap2
seqtk: git clone [email protected]:lh3/seqtk.git
faFilter and faSomeRecords from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/

Run read simulation and mapping, documented in script do_bleties.sh

Evaluations of BleTIES results and comparison with original sequences are in the Jupyter notebooks:

Name		Name	Last commit message	Last commit date
Latest commit History 10 Commits
.gitignore		.gitignore
Evaluate_BleTIES_MILRAA_with_simulated_ONT_R9.5_reads.ipynb		Evaluate_BleTIES_MILRAA_with_simulated_ONT_R9.5_reads.ipynb
Evaluate_BleTIES_MILRAA_with_simulated_PB_reads.ipynb		Evaluate_BleTIES_MILRAA_with_simulated_PB_reads.ipynb
Get_input_IES_coordinates.ipynb		Get_input_IES_coordinates.ipynb
README.md		README.md
do_bleties.sh		do_bleties.sh