Bioinformatics Databases - Revision history

Jordan: /* Installed Bioinformatics Databases */

2026-05-11T19:38:43Z

Installed Bioinformatics Databases

← Older revision		Revision as of 15:38, 11 May 2026
Line 82:		Line 82:
	\|no		\|no
	\|-		\|-
	\|bowtie2		\|[[Bowtie2-Sapelo2 \| bowtie2]]
	\|09/12/2024		\|09/12/2024
	\|no		\|no
	\|-		\|-
	\|Bracken		\|[[Bracken-Sapelo2 \| Bracken]]
	\|08/27/2025		\|08/27/2025
	\|no		\|no
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	\|no		\|no
	\|-		\|-
	\| funannotate \|\| 01/28/2025 (v1.8.17) \|\| no		\| [[Funannotate-Sapelo2 \| funannotate]] \|\| 01/28/2025 (v1.8.17) \|\| no
	\|-		\|-
	\|GAMD		\|GAMD
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	\| humann \|\| 03/26/2023 (v3.6/v3.9) \|\| no		\| humann \|\| 03/26/2023 (v3.6/v3.9) \|\| no
	\|-		\|-
	\| InterProScan \|\| 04/07/2025 (v5.55-88.0) \|\| no		\| [[InterProScan-Sapelo2 \| InterProScan]] \|\| 04/07/2025 (v5.55-88.0) \|\| no
	\|-		\|-
	\|Kraken2 (PlusPF, PlusPFP, PlusPFP-16, core_nt, EuPathDB, GTDB)		\|Kraken2 (PlusPF, PlusPFP, PlusPFP-16, core_nt, EuPathDB, GTDB)

Jordan: /* Installed Bioinformatics Databases */

2026-05-11T19:32:55Z

Installed Bioinformatics Databases

← Older revision		Revision as of 15:32, 11 May 2026
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	! scope="col" \| Module Available		! scope="col" \| Module Available
	\|-		\|-
	\| AlphaFold \|\| 09/03/2023 (v2.3.4) \|\| no		\| [[AlphaFold-Sapelo2 \| AlphaFold]] \|\| 09/03/2023 (v2.3.4) \|\| no
	\|-		\|-
	\| AlphaFold3 \|\| 01/14/2025 ("20241114") \|\| no		\| [[AlphaFold3-Sapelo2 \| AlphaFold3]] \|\| 01/14/2025 ("20241114") \|\| no
	\|-		\|-
	\| AlphaPulldown \|\| 02/28/2025 (v2.0.0) \|\| no		\| AlphaPulldown \|\| 02/28/2025 (v2.0.0) \|\| no

Jordan: /* Installed Bioinformatics Databases */

2026-05-11T19:28:24Z

Installed Bioinformatics Databases

Show changes

Shtsai at 17:12, 31 July 2025

2025-07-31T17:12:19Z

← Older revision		Revision as of 13:12, 31 July 2025
Line 5:		Line 5:
	<code>ml spider ncbiblastdb</code>		<code>ml spider ncbiblastdb</code>

	You can then load a database by running the command module load. For example to load the databases timestamped at 02/02/~~2024~~:		You can then load a database by running the command module load. For example to load the databases timestamped at 05/02/2025:

	<code>module load ncbiblastdb/~~20240202~~</code>		<code>module load ncbiblastdb/20250502</code>

	Loading this module sets the environment variable BLASTDB to /db/ncbiblast/~~20240202~~. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:		Loading this module sets the environment variable BLASTDB to /db/ncbiblast/20250502. This allows BLAST+ to search that directory for databases. You can then use the name of the database you would like to use.(nt, nr, etc.) Here is an example of a shell script to run BLAST+ on the batch queue using the database nt:

	<div class="gscript2">		<div class="gscript2">
Line 24:		Line 24:

	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	module load BLAST+/2.13.0-gompi-~~2022a~~<br>		module load BLAST+/2.16.0-gompi-2024a<br>
	module load ncbiblastdb/~~20240202~~<br>		module load ncbiblastdb/20250502<br>
	blastn -query example.fasta -out results.out -db nt<br>		blastn -query example.fasta -out results.out -db nt<br>
	</div>		</div>

Jordan: /* Installed Bioinformatics Databases */

2025-04-25T19:10:59Z

Installed Bioinformatics Databases

← Older revision		Revision as of 15:10, 25 April 2025
Line 106:		Line 106:
	\| kegg \|\| 09/09/2016 \|\| no		\| kegg \|\| 09/09/2016 \|\| no
	\|-		\|-
	\|Kraken2 (PlusPF, PlusPFP, core_nt, EuPathDB)		\|Kraken2 (PlusPF, PlusPFP, PlusPFP-16, core_nt, EuPathDB)
	\|05/26/~~2024~~		\|04/06/2025
	\|~~yes~~		\|no
	\|-		\|-
	\| maker \|\| 05/22/2018 (v2.31.9) \|\| yes		\| maker \|\| 05/22/2018 (v2.31.9) \|\| yes

Jordan: /* Installed Bioinformatics Databases */

2025-01-17T20:48:19Z

Installed Bioinformatics Databases

← Older revision		Revision as of 16:48, 17 January 2025
Line 106:		Line 106:
	\| kegg \|\| 09/09/2016 \|\| no		\| kegg \|\| 09/09/2016 \|\| no
	\|-		\|-
	\|Kraken2 (PlusPF, EuPathDB)		\|Kraken2 (PlusPF, PlusPFP, core_nt, EuPathDB)
	\|05/26/2024		\|05/26/2024
	\|yes		\|yes

Jordan: /* Installed Bioinformatics Databases */

2024-11-13T19:22:05Z

Installed Bioinformatics Databases

← Older revision		Revision as of 15:22, 13 November 2024
Line 106:		Line 106:
	\| kegg \|\| 09/09/2016 \|\| no		\| kegg \|\| 09/09/2016 \|\| no
	\|-		\|-
	\|Kraken2 (PlusPF)		\|Kraken2 (PlusPF, EuPathDB)
	\|05/26/2024		\|05/26/2024
	\|yes		\|yes

Jordan: /* Installed Bioinformatics Databases */

2024-09-23T20:43:14Z

Installed Bioinformatics Databases

← Older revision		Revision as of 16:43, 23 September 2024
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	\| [[bowtie2\|hg19,mm10 & mm9]] \|\| 07/29/2016 \|\| no		\| [[bowtie2\|hg19,mm10 & mm9]] \|\| 07/29/2016 \|\| no
	\|-		\|-
	\| ~~cellranger~~ \|~~\| 10~~/29/~~2019 \|~~\| no		\|bowtie2
			\|09/12/2024
			\|yes
	\|-		\|-
	\| ~~conspred_ressources~~ \|\| 02/02/~~2017~~ \|\| no		\| cellranger (GRCh38 and MM10) \|\| 12/19/2021 \|\| yes
	\|-		\|-
	\| ~~dammit~~ \|~~\| 03~~/18/~~2021 \|~~\| no		\|CheckV
			\|01/10/2023 (v1.5)
			\|yes
	\|-		\|-
	\| deconseq \|\| 12/01/~~2016~~ \|\| no		\| conspred_ressources \|\| 02/02/2017 \|\| yes
			\|-
			\| dammit \|\| 03/17/2021 (v1.2) \|\| yes
			\|-
			\| deconseq \|\| 12/19/2021 ("04242013") \|\| yes
	\|-		\|-
	\| decontaMiner-Sapelo2\|decontaMiner \|\| 08/29/2019 \|\| no		\| decontaMiner-Sapelo2\|decontaMiner \|\| 08/29/2019 \|\| no
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	\| eggnog-mapper \|\| 04/16/2019 \|\| no		\| eggnog-mapper \|\| 04/16/2019 \|\| no
	\|-		\|-
	\| funannotate \|\| 08/15/~~2019~~ \|\| no		\|foldseek
			\|04/11/2023
			\|yes
			\|-
			\| funannotate \|\| 12/19/2021 \|\| yes
	\|-		\|-
	\| DTDB-Tk \|\| 01/15/2021 \|\| no		\| DTDB-Tk \|\| 01/15/2021 \|\| no
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	\|yes		\|yes
	\|-		\|-
	\| maker \|\| 05/22/2018 \|\| no		\| maker \|\| 05/22/2018 (v2.31.9) \|\| yes
	\|-		\|-
	\| MetaCLADE \|\| 08/29/2019 \|\| no		\| MetaCLADE \|\| 08/29/2019 \|\| no
	\|-		\|-
	\| [[BLAST Databases-Sapelo2 \| NCBI BLAST Databases]] \|\| beginning of every 3 months \|\| yes		\| [[BLAST Databases-Sapelo2 \|NCBI BLAST Databases]] \|\| beginning of every 3 months \|\| yes
			\|-
			\|NCBI-FCS
			\|12/01/2023 (v0.5.0)
			\|yes
	\|-		\|-
	\| [[NCBI Fasta-Sapelo2\|NCBI Fasta]] \|\| 04/06/2022 \|\| yes		\| [[NCBI Fasta-Sapelo2\|NCBI Fasta]] \|\| 04/06/2022 \|\| yes
	\|-		\|-
	\| ngs \|\| 11/03/2016 \|\| no		\| ngs (canine and mouse) \|\| 11/03/2016 \|\| yes
	\|-		\|-
	\| nndb \|\| 04/29/~~2020~~ \|\| no		\| nndb \|\| 05/03/2008 \|\| yes
	\|-		\|-
	\| PB \|\| 04/24/2019 \|\| no		\| PB \|\| 04/24/2019 \|\| no
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	\| [[PfamDB-Sapelo2\|pfam]] \|\| 10/07/2021 \|\| no		\| [[PfamDB-Sapelo2\|pfam]] \|\| 10/07/2021 \|\| no
	\|-		\|-
	\| ~~pylosift~~ \|\| 07/20/2020 \|\| no		\| phylosift \|\| 07/20/2020 \|\| no
	\|-		\|-
	\| [[Refseq-Sapelo2\|Refseq_genomic]] \|\| \|\| no		\| [[Refseq-Sapelo2\|Refseq_genomic]] \|\| \|\| no
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	\| repbase \|\| 01/09/2017 \|\| no		\| repbase \|\| 01/09/2017 \|\| no
	\|-		\|-
	\| rfam \|\| 02/09/2017 \|\| no		\| rfam \|\| 02/01/2017 (v12.2) \|\| yes
	\|-		\|-
	\| seqdb \|\| 05/23/~~2019~~ \|\| no		\| seqdb \|\| 05/22/2012 \|\| yes
	\|-		\|-
	\| sortmerna \|\| 02/02/~~2021~~ \|\| no		\| sortmerna \|\| 03/04/2016 \|\| no
	\|-		\|-
	\| [[TaxDB-Sapelo2\|~~TaxDB~~]] \|\| 02/26/2019 \|\| no		\| [[TaxDB-Sapelo2\|taxdb]] \|\| 02/23/2019 \|\| yes
	\|-		\|-
	\| topcons2 \|\| 02/18/2021 \|\| no		\| topcons2 \|\| 02/18/2021 \|\| no
	\|-		\|-
	\| [[Uniprot-Sapelo2\|Uniprot]] \|\| 11/19/~~2020~~ \|\| no		\| [[Uniprot-Sapelo2\|Uniprot]] \|\| 06/15/2023 \|\| yes
	\|-		\|-
	\| [[Uniref-Sapelo2\|Uniref]] \|\| 02/25/2022 \|\| no		\| [[Uniref-Sapelo2\|Uniref]] \|\| 02/25/2022 \|\| yes
			\|-
			\|virulencefinder
			\|05/06/2024
			\|yes
	\|-		\|-
	\| [[wublast-Sapelo2\|wublast]] \|\| 03/01/2020 \|\| no		\| [[wublast-Sapelo2\|wublast]] \|\| 04/01/2020 \|\| no
	\|-		\|-
	\|}		\|}

Jordan: /* Installed Bioinformatics Databases */

2024-09-13T20:22:02Z

Installed Bioinformatics Databases

← Older revision		Revision as of 16:22, 13 September 2024
Line 94:		Line 94:
	\| kegg \|\| 09/09/2016 \|\| no		\| kegg \|\| 09/09/2016 \|\| no
	\|-		\|-
	\|Kraken2		\|Kraken2 (PlusPF)
	\|~~PlusPF (~~05/26/2024)		\|05/26/2024
	\|yes		\|yes
	\|-		\|-

Jordan: /* Installed Bioinformatics Databases */

2024-09-13T20:12:24Z

Installed Bioinformatics Databases

← Older revision		Revision as of 16:12, 13 September 2024
Line 95:		Line 95:
	\|-		\|-
	\|Kraken2		\|Kraken2
	\|05/26/2024		\|PlusPF (05/26/2024)
	\|yes		\|yes
	\|-		\|-