README.md

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

Analysis

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

• Get_input_IES_coordinates.ipynb
• Evaluate_BleTIES_MILRAA_with_simulated_ONT_R9.5_reads.ipynb
• Evaluate_BleTIES_MILRAA_with_simulated_PB_reads.ipynb