ncbi-genome-download

LTR_retriever — command-line Perl tool for high-accuracy identification of Long Terminal Repeat retrotransposons (LTR-RTs) in plant and eukaryotic genomes. Filters raw LTRharvest and LTR_FINDER candid

2 shared topics • 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

2 shared topics • 2 shared operations

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

2 shared topics • 2 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

2 shared topics • 2 shared operations

SnpEff — fast Java-based variant annotation and effect prediction tool that annotates genomic variants (SNPs, indels, MNPs) with gene impact, protein changes, loss-of-function predictions, and HGVS no

2 shared topics • 2 shared operations