Variant Calling
What: Algorithms that identify differences (mutations) in DNA compared to a reference genome.
Algorithms: DeepVariant, Clair3, GraphTyper, Pepper, Clair3-RNA, Clair3-Trio, Clair3-Nova, ClairS, Clair3-MP
Alignment and Assembly
What: These algorithms map reads to reference genomes (alignment) or build a genome from scratch (assembly).
Algorithms: BWA, Bowtie2, Minimap2, SPAdes, Flye
Phasing
What: Algorithms that determine which variants co-occur on the same chromosome. They are crucial for determining disease risk and heritability.
Algorithms: GFAse, HaplotagLR
Structural Variant Detection
What: Algorithms that find large insertions, deletions, duplications, and rearrangements. These tend to be more difficult than SNPs because of the long reads.
Algorithms: pbsv, Severus, Smoove, SViCT
Gene Expression Quantification
What: Algorithms that count RNA transcripts, either bulk or single cell.
Algorithms: Salmon, Kallisto, STAR
Methylation and Epigenetics
What: Algorithms that detect chemical modifications on DNA.
Algorithms: Bismark, Nanopolish
Metagenomics
What: Algorithms that identify species and functions in mixed microbial samples.
Algorithms: Kraken2, MetaPhlAn, Centrifuge
CRISPR Target Scoring
What: Algorithms that predict guide RNA efficacy + off-target effects.
Algorithms: DeepCRISPR, DeepActiveCRISPR, Elevation
Functional Annotation
What: Algorithms that predict protein function, regulatory regions, or disease linkage.
Algorithms: VEP, SnpEff, AlphaMissense