Biocluster Mirrors

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.