Quick Start

Here we go! No time to waste, let's get the ball rolling! Why are you still reading this?!? Go! Go! Go!

Installation

conda create -y -n bactopia -c conda-forge -c bioconda bactopia
conda activate bactopia

Build Dataset

bactopia datasets

This create a folder ./datasets and will build the following datasets:

• CARD
• VFDB
• RefSeq Mash Sketch
• GenBank Sourmash Signatures
• PLSDB Mash Sketch & BLAST

More information about these datasets is available at Build Datasets.

Run Bactopia!

On the first launch of Bactopia it will install the Conda environments, so expect some delays in doing so!

Single Sample

Paired-End

bactopia --R1 SEQS_R1.fastq.gz \
         --R2 SEQS_R2.fastq.gz \
         --sample SAMPLE_NAME \
         --datasets datasets/ \
         --outdir OUTDIR

In the command above, be sure to replace SEQS_R1.fastq.gz and SEQS_R2.fastq.gz with the name of your FASTQ files. You will also want to replace SAMPLE_NAME with your sample's name and OUTDIR with a directory name you would like to use for results.

Single-End

bactopia --SE SEQS.fastq.gz --sample SAMPLE_NAME --datasets datasets/ --outdir OUTDIR

In the command above, be sure to replace SEQS.fastq.gz with the name of your FASTQ file. You will also want to replace SAMPLE_NAME with your sample's name and OUTDIR with a directory name you would like to use for results.

Multiple Samples

bactopia prepare directory-of-fastqs/ > fastqs.txt
bactopia --samples fastqs.txt --datasets datasets --outdir OUTDIR

In the command above, be sure to replace OUTDIR with a directory name you would like to use for results.