Difference between revisions of "Biocluster Mirrors"

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{| style="width: 900px;  margin: 0 auto" class="wikitable" border="1" cellpadding="1" cellspacing="1"
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{| style='margin: 0 auto' class='wikitable' border='1' cellpadding='1' cellspacing='1'
 
|-
 
|-
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! Data Set
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!Application
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! Website
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!Installed Versions
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! Update Schedule
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!Description
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! File System Path
 
 
|-
 
|-
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| Bioconductor
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|[https://github.com/deepmind/alphafold/ alphafold-db]
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| [http://www.bioconductor.org/ http://www.bioconductor.org/]
+
|20210917<br>20220118<br>20230405<br>20240213
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| Weekly
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|Alphafold Databases
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| /home/mirrors/no_backup/R/bioconductor/
 
 
|-
 
|-
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| Cran
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|[https://github.com/zanglab/bart2 bart2-db]
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| [http://cran.r-project.org/ http://cran.r-project.org/]
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|20240302
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| Weekly
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|Databases for Bart2
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| /home/mirrors/no_backup/R/cran/
 
 
|-
 
|-
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| BLAST DBs
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|[https://busco.ezlab.org/ BUSCO-db]
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| [[Ftp:ftp://ftp.ncbi.nlm.nih.gov/blast/db|ftp.ncbi.nlm.nih.gov/blast/db]]
+
|4
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| Weekly
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|Based on evolutionarily-informed expectations of gene content of near-universal single-copy orthologs, BUSCO metric is complementary to technical metrics like N50.
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| /home/mirrors/NCBI/BLAST_DBS/
 
 
|-
 
|-
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| Uniprot
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|[https://card.mcmaster.ca card-prevalence]
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| [[Ftp:ftp://ftp.uniprot.org/pub/databases/uniprot|ftp.uniprot.org/pub/databases/uniprot]]
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|3.0.6
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| Monthly
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|November 2019 release - 85 pathogens, 116914 resistomes, and 182532 AMR allele sequences based on sequence data acquired from NCBI on July 31, 2019, analyzed using RGI 5.0.0 (DIAMOND homolog detection) and CARD 3.0.7. Includes pre-compiled k-mer classifier data for pathogen-of-origin prediction.
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| /home/mirrors/uniprot/
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|-
−
|  
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|[https://ecogenomics.github.io/CheckM/ checkm-db]
 +
|20150116
 +
|CheckM Database
 +
|-
 +
|[https://github.com/chklovski/CheckM2 checkm2-db]
 +
|20230511
 +
|CheckM2 Database
 +
|-
 +
|[https://portal.nersc.gov/CheckV/ checkv-db]
 +
|1.5
 +
|The main change in v1.5 was to remove putatively non-viral sequences to minimize high-confidence matches to the CheckV database for non-viral sequences.
 +
|-
 +
|[http://huttenhower.sph.harvard.edu/humann2 chocophlan]
 +
|0.1.1
 +
|
 +
|-
 +
|[http://www.molgen.ua.ac.be/bioinfo/projects/clusterblast/clusterblast.htm clusterblast]
 +
|20170105
 +
|
 +
|-
 +
|[https://github.com/nanoporetech/dorado dorado-db]
 +
|20240501
 +
|Databases for dorado
 +
|-
 +
|[https://www.ebi.ac.uk/ena ena]
 +
|20241008
 +
|The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing.
 +
|-
 +
|[https://github.com/steineggerlab/foldseek foldseek-db]
 +
|20230921
 +
|Foldseek computes for each match a simple estimate for the probability that the match is a true positive match given its structural bit score. Here, hits within the same superfamily are TP, hits to another fold are FP, and hits to the same family or to another superfamily are ignored.
 +
|-
 +
|[https://github.com/nextgenusfs/funannotate funannotate-db]
 +
|20220428<br>20240515
 +
|funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Installation, usage, and more information can be found at http://funannotate.readthedocs.io
 +
|-
 +
|[https://software.broadinstitute.org/gatk/download/bundle gatkbundle]
 +
|20191118
 +
|he GATK resource bundle is a collection of standard files for working with human resequencing data with the GATK. We provide several versions of the bundle corresponding to the various reference builds,
 +
|-
 +
|[https://www.ncbi.nlm.nih.gov/genbank/ genbank]
 +
|250
 +
|GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences
 +
|-
 +
|[https://gtdb.ecogenomic.org/ gtdb]
 +
|207<br>214
 +
|GENOME TAXONOMY DATABASE
 +
|-
 +
|[https://github.com/biobakery/humann/ humann-db]
 +
|201901b
 +
|Databases for HUMAnN
 +
|-
 +
|[https://www.ebi.ac.uk/interpro/ interpro]
 +
|68.0<br>101.0<br>102.0
 +
|InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.
 +
|-
 +
|[https://github.com/biobakery/kneaddata KneadData-db]
 +
|20230405
 +
|Databases for KneadData
 +
|-
 +
|[https://benlangmead.github.io/aws-indexes/k2 kraken2-db]
 +
|20220327<br>20230314<br>20240112
 +
|Kraken 2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
 +
|-
 +
|[ftp://ftp.ncbi.nlm.nih.gov/blast/db/ ncbi-blastdb]
 +
|20220318<br>20230124
 +
|BLAST search pages under the Basic BLAST section of the NCBI BLAST home page(http://blast.ncbi.nlm.nih.gov/) use a standard set of BLAST databases for nucleotide, protein, and translated BLAST searches.
 +
|-
 +
|[https://pfam.xfam.org/ pfam]
 +
|32.0<br>35.0<br>37.0
 +
|The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)
 +
|-
 +
|pgap-db
 +
|2021-07-01.build5508
 +
|
 +
|-
 +
|[https://www.ncbi.nlm.nih.gov/refseq/ refseq-db]
 +
|211
 +
|The Reference Sequence (RefSeq) collection provides a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.
 +
|-
 +
|[https://www.arb-silva.de silva]
 +
|138.1
 +
|SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).
 +
|-
 +
|[https://github.com/hyeshik/tailseeker tailseeker-db]
 +
|20161215
 +
|Database Indexes for Tailseeker
 +
|-
 +
|[https://www.uniprot.org/ uniprot]
 +
|2022_05<br>2023_04<br>2024_04<br>2024_05
 +
|The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
 
|}
 
|}

Latest revision as of 03:00, 10 October 2024

Application Installed Versions Description
alphafold-db 20210917
20220118
20230405
20240213 		Alphafold Databases
bart2-db 20240302 Databases for Bart2
BUSCO-db 4 Based on evolutionarily-informed expectations of gene content of near-universal single-copy orthologs, BUSCO metric is complementary to technical metrics like N50.
card-prevalence 3.0.6 November 2019 release - 85 pathogens, 116914 resistomes, and 182532 AMR allele sequences based on sequence data acquired from NCBI on July 31, 2019, analyzed using RGI 5.0.0 (DIAMOND homolog detection) and CARD 3.0.7. Includes pre-compiled k-mer classifier data for pathogen-of-origin prediction.
checkm-db 20150116 CheckM Database
checkm2-db 20230511 CheckM2 Database
checkv-db 1.5 The main change in v1.5 was to remove putatively non-viral sequences to minimize high-confidence matches to the CheckV database for non-viral sequences.
chocophlan 0.1.1
clusterblast 20170105
dorado-db 20240501 Databases for dorado
ena 20241008 The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing.
foldseek-db 20230921 Foldseek computes for each match a simple estimate for the probability that the match is a true positive match given its structural bit score. Here, hits within the same superfamily are TP, hits to another fold are FP, and hits to the same family or to another superfamily are ignored.
funannotate-db 20220428
20240515 		funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Installation, usage, and more information can be found at http://funannotate.readthedocs.io
gatkbundle 20191118 he GATK resource bundle is a collection of standard files for working with human resequencing data with the GATK. We provide several versions of the bundle corresponding to the various reference builds,
genbank 250 GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences
gtdb 207
214 		GENOME TAXONOMY DATABASE
humann-db 201901b Databases for HUMAnN
interpro 68.0
101.0
102.0 		InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.
KneadData-db 20230405 Databases for KneadData
kraken2-db 20220327
20230314
20240112 		Kraken 2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
ncbi-blastdb 20220318
20230124 		BLAST search pages under the Basic BLAST section of the NCBI BLAST home page(http://blast.ncbi.nlm.nih.gov/) use a standard set of BLAST databases for nucleotide, protein, and translated BLAST searches.
pfam 32.0
35.0
37.0 		The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)
pgap-db 2021-07-01.build5508
refseq-db 211 The Reference Sequence (RefSeq) collection provides a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.
silva 138.1 SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).
tailseeker-db 20161215 Database Indexes for Tailseeker
uniprot 2022_05
2023_04
2024_04
2024_05 		The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
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