ARIBA

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

gffread -- GFF/GTF utility for filtering, converting, and extracting sequences from genome annotation files. Converts between GFF3 and GTF formats, extracts transcript (FASTA) and protein sequences fr

1 shared topic • 1 shared operation

Haploflow is a C++ de novo assembler for strain-resolved viral haplotype reconstruction from mixed quasispecies sequencing data. It applies minimum-flow decomposition on a de Bruijn graph to recover i

1 shared topic • 1 shared operation

hifiasm — fast haplotype-resolved de novo assembler for PacBio HiFi reads, producing phased telomere-to-telomere genome assemblies. Supports HiFi-only, Hi-C integrated, trio-binning, and ultralong ONT

1 shared topic • 1 shared operation