For all of our downstream bioinformatic processing, we use open source software and scripts that are meticulously documented and can easily be reproduced by the user. The first step for any analysis we do is to trim and quality filter the sequencing reads. We provide the user with all pre- and post-processing quality check statistics. After QA/QC several options are available:
We have a robust pipeline for calling single nucleotide polymorphisms (SNPs), short insertions and deletions (indels), and structural variants. Importantly, collectively we have decades of experience calling variants in single isolates and in whole populations. We provide easy to read and interpret summary tables of all predicted mutations alongside the raw data. To learn more about the primary software we use to call mutations please see: http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/doc....
Determination of Isolate Speciation or Relatedness
We offer taxonomic assignment, phylogenic reconstruction, and multi-locus sequence typing (MLST) analyses on whole genome isolates. For clinically relevant data, we start with the nullarbor software (https://github.com/tseemann/nullarbor) and refine based on the needs of the user. For other sequence data, including environmental isolates, we use a series of different taxonomic assignment algorithms based on marker gene phylogenies and whole genome alignments.
Genome/Metagenome Assemblies and Annotations
We offer annotated genome assemblies in a variety of formats (fasta, genbank, etc.). The type of assemblies and annotations depend on the sample and the desired product. We work closely with the user to understand and deliver the best fit for the study.
Antibiotic Resistant Gene Prediction
We run the sequences through a number of different antibiotic resistance gene databases (e.g. CARD, https://card.mcmaster.ca/) to predict the presence/absence of antibiotic resistance genes.