We run standard bioinformatics workflows on sequencing and genomic data, including:
- Microbial genome resequencing — variant calling, contamination screening, and mutation profiling in bacteria, including adaptive laboratory evolution experiments (breseq).
- Eukaryotic variant analysis — germline and somatic SNP calling in yeast and fungi (GATK).
- Deep amplicon and long-read variant analysis — detection of low-frequency variants in mixed populations, haplotype phasing, and linkage between co-occurring mutations. For example, we use this analysis to map compensatory mutations in viral populations from PacBio HiFi data.
- Sequence discovery in metagenomic and viral data — detection of divergent sequences, including deep-learning search for novel viral polymerases.
- Standard sequencing workflows — read quality control, assembly and assembly QC, RNA-seq quantification, taxonomic profiling, variant annotation, and phylogenetics.