Nextstrain

vConTACT2 (Viral Contig Automatic Cluster Taxonomy 2) clusters prokaryotic viral genomes and contigs by shared protein content to assign taxonomy context from reference viral genomes. Use when working

2 shared topics • 1 shared operation

BWA-MEM2 — accelerated Burrows-Wheeler Aligner for mapping short DNA reads to reference genomes. Use when aligning Illumina WGS, WES, targeted panel, ChIP-seq, or ATAC-seq FASTQ reads. Drop-in replace

1 shared topic • 1 shared operation

Ensembl Database — EMBL-EBI's comprehensive genome annotation database covering 300+ species with gene models, variants, regulatory features, and comparative genomics. Query via REST API at rest.ensem

1 shared topic • 1 shared operation

GATK HaplotypeCaller — germline short variant caller using localized de novo assembly of haplotypes. Calls SNPs and indels from BAM/CRAM alignment files, producing VCF or gVCF output. Supports single-

1 shared topic • 1 shared operation

OrthoFinder — fast, accurate ortholog inference for comparative genomics. Identifies orthogroups, orthologs, gene trees, rooted species trees, and gene duplication events from protein or nucleotide se

1 shared topic • 1 shared operation