UCSC Kent Utilities

CrossMap is a Python tool for genome coordinate liftover — converting genomic positions between different genome assemblies (e.g., hg19 to hg38, GRCh37 to GRCh38, mm9 to mm10). Supports BED, BAM/SAM/C

1 shared topic • 3 shared operations

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 • 3 shared operations

Liftoff — accurate genome annotation liftover tool that maps GFF/GTF annotations between assemblies of the same or closely-related species using Minimap2 alignment. Supports gene copy detection, ORF v

1 shared topic • 3 shared operations

MAKER — portable genome annotation pipeline that integrates ab initio gene predictors (SNAP, Augustus, GeneMark), protein and EST evidence alignment, and repeat masking to produce GFF3 gene models wit

1 shared topic • 3 shared operations

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 • 2 shared operations