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	343	June 12, 2025
Kaiju database request usegalaxy.eu support reference-index , tool-help , kaiju_kaiju	13	149	June 18, 2026
Adding nt_core db to Bracken and related workflow tools usegalaxy.eu support reference-index , kraken2 , bracken	8	196	June 17, 2026
Resistance gene identifier (RGI) version incompatible with latest CARD database usegalaxy.org support reference-index , tool-dev	3	41	May 27, 2026
Kraken2 databases question reference-index , tool-help , kraken2	1	31	April 29, 2026
Request Adding Salmonella cgMLST (3002 loci) scheme for CoreProfiler allele_calling usegalaxy.org support reference-index , coreprofiler_allele_calling	1	50	April 22, 2026
Adding the tardigrade (H. exemplaris) genome to Galaxy reference-index , igv , reference-genome	3	208	April 7, 2026
Taxonomic classification using Kraken2 reference-index , kraken2	2	42	March 16, 2026
Bad lineage by Nextclade usegalaxy.eu support reference-index , variant-analysis	2	14	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	43	February 19, 2026
Use GTDB-Tk database: Navigating tool versions usegalaxy.org support tool-version , reference-index , troubleshooting , resources	1	66	January 30, 2026
Missing Pfam-A reference data in Galaxy PfamScan reference-index , tool-help , pfamscan	1	27	January 23, 2026
Building kraken2 + gtdb? usegalaxy.org support reference-index , resources , tool-help , kraken2	5	94	December 26, 2025
Can usegalaxy.eu provide latest Kraken2 core_nt databases? usegalaxy.eu support reference-index , kraken2	3	82	December 11, 2025
Request for the add of genome reference-index , custom-genome , custom-build , resources	1	29	December 10, 2025
HUMAnN Cached database with clade-specific marker genes devops-administration , reference-index , galaxy-local , humann	11	535	December 8, 2025
RSEM prepare reference usegalaxy.eu support reference-index , tool-help , rsem_prepare_reference	5	146	October 9, 2025
Update to InterProScan database in InterProScan functional annotation tool at usegalaxy.eu? usegalaxy.eu support reference-index , interproscan	1	44	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	51	August 5, 2025
GeNomad database usegalaxy.org support reference-index	7	127	July 11, 2025
Want to add a new organism for HISAT2 analysis usegalaxy.org support reference-index , reference-annotation , reference-genome	1	38	June 12, 2025
Updating CARD database usegalaxy.eu support reference-index , tool-help , abricate	2	210	May 6, 2025
Editing a workflow to choose a different reference genome usegalaxy.org.au support gtn-tutorial , workflow , reference-index , troubleshooting	6	163	April 23, 2025
GTDB-Tk database update to current version usegalaxy.eu support reference-index , gtdbtk_classify_wf , microgalaxy	2	61	April 23, 2025
Bakta database update usegalaxy.eu support reference-index , development-tools , microgalaxy , bakta	1	50	April 17, 2025
Request to update BLASTP nr database usegalaxy.eu support reference-index , blastp	5	96	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	10	192	March 14, 2025
New data manager for clair3 models usegalaxy.org support tool-install , reference-index	1	68	February 24, 2025
GTDB-Tk use and binning contigs usegalaxy.org support reference-index , gtdbtk_classify_wf , microgalaxy	4	200	February 21, 2025
Eukaryote taxonomic classification reference database options usegalaxy.org support reference-index , gtdbtk_classify_wf , microgalaxy , bracken	13	325	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…