Topics tagged reference-index

Topic	Replies	Views	Activity
FAQ: NCBI reference data Resources reference-index , reference-annotation , reference-genome , resources :speech_balloon: How to find NCBI Reference data? Q: Where can I find the URL links to a reference genome FASTA, annotation, or GenBank file? A: Use the NCBI Genome Assembly page for the organism of interest — for examp…	0	175	June 12, 2025
HUMAnN Cached database with clade-specific marker genes reference-index , galaxy-local	11	373	December 8, 2025
RSEM prepare reference usegalaxy.eu support reference-index , tool-help , rsem_prepare_reference	5	70	October 9, 2025
Update to InterProScan database in InterProScan functional annotation tool at usegalaxy.eu? usegalaxy.eu support reference-index	1	26	October 8, 2025
Newly launched BN rat genome assembly GRCr8 into the reference genome list? usegalaxy.eu support reference-index , custom-genome , reference-annotation , reference-genome	1	31	August 5, 2025
GeNomad database usegalaxy.org support reference-index	7	99	July 11, 2025
Want to add a new organism for HISAT2 analysis usegalaxy.org support reference-index , reference-annotation , reference-genome	1	24	June 12, 2025
Updating CARD database usegalaxy.eu support reference-index , tool-help , abricate	2	119	May 6, 2025
Editing a workflow to choose a different reference genome usegalaxy.org.au support gtn-tutorial , workflow , reference-index , troubleshooting	6	86	April 23, 2025
GTDB-Tk database update to current version usegalaxy.eu support reference-index , gtdbtk_classify_wf , microgalaxy	2	37	April 23, 2025
Bakta database update usegalaxy.eu support reference-index , tool-dev , microgalaxy , bakta	1	34	April 17, 2025
Request to update BLASTP nr database usegalaxy.eu support reference-index , blastp	5	37	March 14, 2025
Getting NCBI Reference genome indexed for tools: custom genome, reference genome, reference annotation reference-index , custom-genome , reference-annotation , reference-genome , featurecounts , reference-transcriptome	11	103	July 22, 2025
New data manager for clair3 models usegalaxy.org support tool-install , reference-index	1	40	February 24, 2025
GTDB-Tk use and binning contigs usegalaxy.org support reference-index , gtdbtk_classify_wf , microgalaxy	4	130	February 21, 2025
Eukaryote taxonomic classification reference database options usegalaxy.org support reference-index , gtdbtk_classify_wf , microgalaxy , bracken	16	207	February 19, 2025
Kraken2 and Bracken databases update usegalaxy.eu support reference-index , bracken	4	52	February 19, 2025
Bracken database missed usegalaxy.eu support reference-index , kraken2 , bracken	2	45	February 19, 2025
Request to upload/add new version of reference genome of Aedes albopictus (Genome assembly AalbF5) usegalaxy.org support reference-index , custom-genome , reference-annotation , reference-genome , reference-transcriptome	1	31	February 19, 2025
Kraken2 new Core-nt reference usegalaxy.org support reference-index	6	72	February 18, 2025
Converting Metaphlan SGBs to GTDB reference-index , gtdbtk_classify_wf , microgalaxy	2	396	February 14, 2025
GTDB-Tk Classify genomes reference-index , metagenomics , tool-help , gtdbtk_classify_wf , microgalaxy , evolution	3	457	February 14, 2025
Database missing for GTDB-Tk tool usegalaxy.eu support reference-index , gtdbtk_classify_wf , microgalaxy	4	111	February 14, 2025
gtdbtk_classify_wf Missing Database! usegalaxy.eu support reference-index , gtdbtk_classify_wf , microgalaxy	3	92	February 14, 2025
Adding nt_core db to Bracken and related workflow tools usegalaxy.eu support reference-index , kraken2 , bracken	7	120	February 4, 2025
usegalaxy.eu cufflinks no cached reference data usegalaxy.eu support reference-index	6	57	January 24, 2025
Chlamydomonas genome usegalaxy.org support reference-index	1	21	January 22, 2025
ncbi fcs gx database not available in eu but on org reference-index	2	142	January 8, 2025
Kraken 2 core nt database and large amount of unclassified reads? usegalaxy.eu support reference-index , single-cell	6	635	January 8, 2025
Built-in reference genome of domestic water buffalo usegalaxy.org.au support reference-index , reference-annotation , reference-genome	1	44	January 6, 2025

FAQ: NCBI reference data

:speech_balloon: How to find NCBI Reference data? Q: Where can I find the URL links to a reference genome FASTA, annotation, or GenBank file? A: Use the NCBI Genome Assembly page for the organism of interest — for examp…