Odontosyllis undecimdonta luciferase

This repository contains analyses required to recreate the analyses found in Schultz, Kotlobay, et al. 2018

Specifically, it contains the scripts to recreate figure 2 (the transcript alignment figure), as well as the orthology search with other polychaetes.

Figure 2

Requirements:

This is a reproducible pipeline assuming that all of the required software and sequencing reads are on your file system.

Required software:

• Python 3.x - I recommend Anaconda
• Snakemake
• Trimmomatic v0.35
• a local copy of the NCBI nr database
• a local operating version of blast
• pauvre plotting software
• the Trinity RNAseq assembler docker
• bioawk and normal awk
• hisat2
• bwa
• samtools
• minimap2

How to run

For now you will need to edit config.yaml and specify the location of the reads files from O. undecimdonta sequencing project on ENA/SRA. An automatic download feature will be added when the reads become available.

After install all of the required software above, download this repository and execute the following commands:

git clone https://github.com/conchoecia/odontosyllis_undecimdonta_luciferase.git
cd odontosyllis_undecimdonta_luciferase/
snakemake --cores <desired number of cores>

This analysis took approximately 10 days on a linux server with 90 threads. Most of the computation time is spent assembling transcriptomes.