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	300	June 12, 2025
Kraken2 databases question reference-index , tool-help , kraken2	1	22	April 29, 2026
Request Adding Salmonella cgMLST (3002 loci) scheme for CoreProfiler allele_calling usegalaxy.org support reference-index , coreprofiler_allele_calling	1	42	April 22, 2026
Adding the tardigrade (H. exemplaris) genome to Galaxy reference-index , igv , reference-genome	4	205	April 7, 2026
Taxonomic classification using Kraken2 reference-index , kraken2	2	31	March 16, 2026
Bad lineage by Nextclade usegalaxy.eu support reference-index , variant-analysis	2	8	March 6, 2026
Genome update sus scro: how to use a custom genome! usegalaxy.org support reference-index , custom-genome , troubleshooting , reference-annotation , reference-genome , custom-build	2	20	February 19, 2026
Use GTDB-Tk database: Navigating tool versions usegalaxy.org support tool-version , reference-index , troubleshooting , resources	1	41	January 30, 2026
Missing Pfam-A reference data in Galaxy PfamScan reference-index , tool-help , pfamscan	1	23	January 23, 2026
Building kraken2 + gtdb? usegalaxy.org support reference-index , resources , tool-help , kraken2	6	62	April 29, 2026
Can usegalaxy.eu provide latest Kraken2 core_nt databases? usegalaxy.eu support reference-index , kraken2	3	67	December 11, 2025
Request for the add of genome reference-index , custom-genome , custom-build , resources	1	23	December 10, 2025
HUMAnN Cached database with clade-specific marker genes devops-administration , reference-index , galaxy-local , humann	12	509	March 17, 2026
RSEM prepare reference usegalaxy.eu support reference-index , tool-help , rsem_prepare_reference	5	115	October 9, 2025
Update to InterProScan database in InterProScan functional annotation tool at usegalaxy.eu? usegalaxy.eu support reference-index , interproscan	1	39	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	46	August 5, 2025
GeNomad database usegalaxy.org support reference-index	7	121	July 11, 2025
Want to add a new organism for HISAT2 analysis usegalaxy.org support reference-index , reference-annotation , reference-genome	1	36	June 12, 2025
Updating CARD database usegalaxy.eu support reference-index , tool-help , abricate	3	194	April 7, 2026
Editing a workflow to choose a different reference genome usegalaxy.org.au support gtn-tutorial , workflow , reference-index , troubleshooting	6	145	April 23, 2025
GTDB-Tk database update to current version usegalaxy.eu support reference-index , gtdbtk_classify_wf , microgalaxy	2	59	April 23, 2025
Bakta database update usegalaxy.eu support reference-index , development-tools , microgalaxy , bakta	1	44	April 17, 2025
Request to update BLASTP nr database usegalaxy.eu support reference-index , blastp	5	75	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	159	July 22, 2025
New data manager for clair3 models usegalaxy.org support tool-install , reference-index	1	63	February 24, 2025
GTDB-Tk use and binning contigs usegalaxy.org support reference-index , gtdbtk_classify_wf , microgalaxy	4	177	February 21, 2025
Eukaryote taxonomic classification reference database options usegalaxy.org support reference-index , gtdbtk_classify_wf , microgalaxy , bracken	16	299	February 19, 2025
Kraken2 and Bracken databases update usegalaxy.eu support reference-index , bracken	4	62	February 19, 2025
Bracken database missed usegalaxy.eu support reference-index , kraken2 , bracken	2	57	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	42	February 19, 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…