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riboSeed - quickstart

Too Impatient for the quickstart? See our Especially Quickstart Guide

Overview

In this guide, I will walk you through a typical experiment.

Requirements

conda install riboseed

Get the Data

Let's try using riboSeed on Listeria monocytogenes. We will use the SRA toolkit's fastq-dump tool to get the data:

fastq-dump --split-files SRR5181495

That takes a while to download.

Read 618654 spots for SRR5181495
Written 618654 spots for SRR5181495

Let's use the Listeria monocytogenes str. 4b F2365 genome as reference, NCBI accession AE017262.2. Download this :

wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/285/GCF_000008285.1_ASM828v1/GCF_000008285.1_ASM828v1_genomic.fna.gz
# unzip it
gunzip GCF_000008285.1_ASM828v1_genomic.fna.gz
# rename it something slightly shorter
mv GCF_000008285.1_ASM828v1_genomic.fna  AE017262.2.fasta

ribo run

Now that we have the reference as a fasta file and our reads, lets run the pipeline:

$ ribo run -r ./AE017262.2.fasta -F ./SRR5181495_1.fastq -R ./SRR5181495_2.fastq  --cores 4 --threads 1 -v 1 --serialize -o ./listeria_riboSeed_output/

Evaluate

Use MAUVE to visualize the assemblies found in ./seed_output/final_de_novo_assembly and ./seed_output/final_de_fere_novo_assembly. You should see that 4 out of the 6 regions were bridged. The remaining region consists of a tandem rDNA repeat, which is a continuing problem for rDNA assembly. Looking at the riboSelect output, we can see that it has chosen 6 clusters. We can try to treat the tandem clusters as one (for a total of 5 clusters) by re-running ribo run with --clusters 5.