Repositories in Category Data Managers
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Type
Metadata
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Owner
amrfinderplus_data_manager_build
Install AMRfinderplus databases for amrfinderplus or bakta tools
Unrestricted
2 (2024-05-30)
1 (2023-04-16)
iuc
checkm2_build_database
Data manager for CheckM2 reference data
Unrestricted
2 (2025-02-19)
1 (2025-01-19)
iuc
checkv_build_database
Data managers for CheckV reference data
Unrestricted
3 (2024-12-18)
2 (2024-11-18)
1 (2024-09-20)
0 (2024-09-16)
ufz
cravat_annotate_mutations
Returns CRAVAT annotation
Unrestricted
30 (2018-07-18)
29 (2018-07-18)
28 (2018-07-18)
27 (2018-07-18)
26 (2018-07-18)
25 (2018-07-18)
24 (2018-07-18)
23 (2018-07-18)
22 (2018-06-27)
21 (2018-06-27)
20 (2018-06-12)
19 (2018-06-12)
18 (2018-06-12)
17 (2018-06-12)
16 (2018-06-12)
15 (2018-06-12)
14 (2018-06-12)
12 (2018-06-12)
11 (2018-06-12)
in_silico
cravat_score_and_annotate
Creates a job in CRAVAT
Unrestricted
21 (2018-08-16)
20 (2018-08-16)
19 (2018-08-16)
18 (2018-08-16)
17 (2018-08-16)
16 (2018-08-16)
15 (2018-07-30)
14 (2018-07-30)
13 (2018-07-30)
12 (2018-07-30)
11 (2018-06-27)
10 (2018-06-27)
9 (2018-06-12)
8 (2018-06-12)
7 (2018-06-12)
in_silico
ctat_centrifuge_indexes_data_manager
Facilitates the download and/or specification of the location of a centrifuge index.
Unrestricted
0
(2018-07-16)
trinity_ctat
ctat_genome_resource_libs_data_manager
Download, build, or set the location of a CTAT Genome Resource Library.
Unrestricted
1 (2018-11-11)
0 (2018-07-16)
trinity_ctat
ctat_lncrna_annotations_data_manager
Retrieve and/or specify the location of CTAT lncrna annotations files.
Unrestricted
0
(2018-07-16)
trinity_ctat
cut_include_exclude
Simplify use of cut. Simply remove or keep selected column.
Unrestricted
2
(2015-12-16)
r-lannes
data_manager_all_fasta_path
Creates a link in the all_fasta data table to a fasta file on the server
Unrestricted
0
(2016-05-07)
brenninc
data_manager_amrfinderplus
Data Manager for NCBI AMRFinderPlus
Unrestricted
14 (2025-03-17)
12 (2022-05-24)
estrain
data_manager_bakta
Install Bakta databases for bakta genome annotation
Unrestricted
6 (2024-06-20)
5 (2024-06-05)
4 (2023-08-25)
3 (2023-06-23)
2 (2023-04-16)
iuc
data_manager_bowtie2_index_builder
Data Manager for building bowtie2 indexes
Unrestricted
11 (2024-12-05)
10 (2023-04-16)
8 (2020-11-22)
5 (2019-12-04)
4 (2019-05-09)
3 (2017-04-04)
2 (2015-11-16)
1 (2015-08-10)
0 (2015-04-14)
devteam
data_manager_bowtie_index_builder
Data Manager for building bowtie indexes
Unrestricted
8 (2024-12-05)
7 (2024-05-21)
6 (2023-04-16)
3 (2017-04-04)
1 (2016-09-18)
iuc
data_manager_build_alfa_indexes
Build ALFA indexes from automatically downloaded gtf annotation file
Unrestricted
0
(2018-05-16)
biocomp-ibens
data_manager_build_bracken_database
Contains data managers that define and populate the bracken_databases tool data table.
Unrestricted
6 (2024-03-06)
4 (2023-04-16)
2 (2020-11-22)
iuc
data_manager_build_bracken_database
Contains data managers that define and populate the bracken_databases tool data table.
Unrestricted
0
(2019-10-24)
dfornika
data_manager_build_kma_index
Data Manager for building KMA indexes
Unrestricted
2
(2020-11-22)
iuc
data_manager_build_kraken2_database
Contains data managers that define and populate the kraken2_databases tool data table.
Unrestricted
15 (2025-01-25)
14 (2024-12-13)
13 (2024-11-15)
12 (2024-10-18)
11 (2024-07-15)
10 (2024-06-13)
9 (2024-06-06)
8 (2023-12-18)
7 (2023-04-16)
5 (2021-11-08)
3 (2020-11-22)
1 (2019-08-03)
0 (2019-05-30)
iuc
data_manager_build_kraken2_database
Contains data managers that define and populate the kraken2_databases tool data table.
Unrestricted
19 (2019-10-23)
18 (2019-05-24)
16 (2019-03-05)
11 (2019-03-05)
6 (2019-03-04)
1 (2019-02-28)
dfornika
data_manager_build_kraken2_database
Contains data managers that define and populate the kraken2_databases tool data table.
Unrestricted
0
(2020-12-01)
dave
data_manager_build_kraken_database
Contains a data manager that defines and populates the kraken_databases tool data table.
Unrestricted
8 (2024-05-21)
7 (2023-04-16)
4 (2018-07-17)
2 (2017-04-04)
1 (2016-06-14)
0 (2015-07-23)
devteam
data_manager_build_staramr
Download the Resfinder, Pointfinder and Plasmidfinder databases for staramr search command
Unrestricted
1 (2025-02-27)
0 (2025-01-16)
iuc
data_manager_bwa_mem2_index_builder
Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.
Unrestricted
1 (2024-12-05)
0 (2024-09-30)
iuc
data_manager_bwa_mem_index_builder
Data Manager for building BWA (0.6+) indexes
Unrestricted
10 (2024-12-05)
9 (2023-04-16)
6 (2019-11-18)
5 (2017-04-04)
3 (2016-04-26)
2 (2015-08-26)
devteam
data_manager_bwameth_index_builder
bwa-meth is a fast and accurate aligner for BS-seq data
Unrestricted
6 (2020-11-22)
4 (2019-10-01)
3 (2017-09-21)
iuc
data_manager_cat
Contig Annotation Tool (CAT) Data Manager
Unrestricted
2 (2023-12-18)
1 (2020-11-22)
iuc
data_manager_clair3_models
Install Clair3 models from the Oxford Nanopore Rerio repository
Unrestricted
0
(2025-02-20)
iuc
data_manager_coast_taxonomic_filters
Data Manager for the taxonomic filters used by COAST in BLAST based runs
Unrestricted
0
(2021-07-15)
diodupima
data_manager_dada2
Data manager to download DADA2 reference databases
Unrestricted
7 (2024-05-21)
6 (2023-06-27)
5 (2021-08-03)
4 (2020-11-22)
2 (2020-03-29)
1 (2019-12-05)
0 (2019-11-08)
iuc
data_manager_deeparg
Download deepARG database
Unrestricted
1 (2025-03-11)
0 (2025-02-07)
iuc
data_manager_defense_finder
Download defense finder models.
Unrestricted
2 (2025-02-13)
1 (2023-10-11)
0 (2023-09-12)
rplanel
data_manager_diamond_database_builder
Pre-generate indexes for Diamond
Unrestricted
5 (2023-12-18)
4 (2021-12-08)
3 (2021-12-07)
1 (2019-12-03)
0 (2015-02-08)
bgruening
data_manager_dram_database_downloader
DRAM for distilling microbial metabolism to automate the curation of microbiome function
Unrestricted
1
(2022-09-13)
iuc
data_manager_fetch_busco
Contains a data manager that defines and populates the busco tool data table.
Unrestricted
3 (2025-02-20)
2 (2023-04-24)
1 (2020-11-22)
iuc
data_manager_fetch_gene_annotation
Contains a data manager that defines and populates the gene_annotation data table.
Unrestricted
48 (2024-05-21)
47 (2020-11-22)
45 (2016-07-08)
scottx611x
data_manager_fetch_genome_dbkeys_all_fasta
Allows optionally defining a new DBKEY and retrieves a FASTA file and populate the all_fasta.loc data table.
Unrestricted
10 (2024-12-05)
9 (2019-12-05)
8 (2019-10-16)
7 (2017-06-15)
2 (2015-10-14)
devteam
data_manager_fetch_gff
Data manager to handle GFF files associated with genome builds
Unrestricted
5
(2018-11-15)
ieguinoa
data_manager_fetch_index_maf
Fetch and index multiple alignments from UCSC
Unrestricted
1
(2020-11-22)
iuc
data_manager_fetch_index_maf
Download and index a MAF from UCSC
Unrestricted
1 (2020-07-15)
0 (2020-07-15)
dave
data_manager_fetch_ncbi_taxonomy
Contains a data manager that defines and populates the ncbi_taxonomy tool data table.
Unrestricted
7 (2024-05-21)
6 (2021-03-19)
5 (2020-11-22)
4 (2020-07-06)
3 (2020-07-06)
2 (2020-04-28)
1 (2017-04-04)
devteam
data_manager_fetch_plasmidfinder
Install PlasmidFinder databases
Unrestricted
2 (2024-06-06)
1 (2023-08-25)
0 (2023-06-15)
iuc
data_manager_fetch_refseq
Fetch FASTA data from NCBI RefSeq and update all_fasta data table
Unrestricted
4 (2020-11-22)
2 (2019-11-28)
1 (2019-01-13)
iuc
data_manager_fetch_tx2gene
Load entries in tx2gene table with transcript to gene tables or GTF/GFF file.
Unrestricted
5 (2021-06-07)
1 (2018-10-10)
ieguinoa
data_manager_for_directory_data
Loads a Directory and Extension Pair into the directory_data Data Table
Unrestricted
0
(2016-05-07)
brenninc
data_manager_frogs
FROGS data manager
Unrestricted
0
(2021-08-23)
frogs
data_manager_funannotate
Install funannotate databases for funannotate tool
Unrestricted
5 (2025-03-07)
4 (2025-03-07)
3 (2021-11-19)
1 (2021-11-18)
0 (2021-08-26)
iuc
data_manager_funannotate_options
Install funannotate databases for funannotate tool
Unrestricted
0
(2025-03-09)
iuc
data_manager_gatk_picard_index_builder
Data Manager for building gatk picard indexes
Unrestricted
7 (2024-05-21)
6 (2023-04-16)
4 (2020-11-22)
devteam
data_manager_gemini_database_downloader
GEMINI: a flexible framework for exploring genome variation
Unrestricted
9 (2022-12-03)
8 (2020-11-22)
5 (2018-12-19)
3 (2017-04-04)
2 (2016-02-18)
1 (2014-08-26)
0 (2014-08-25)
iuc
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