Tutorial

Tutorial using pre-built marine microbial genome database:

1. Download the backup database file for the pre-built database the working directory: Database File.
2. Picking up after step 3 from the Installation Instructions, rebuild this database into the "metatryp2_proteins" empty database you just created.

sudo -u postgres pg_restore  --dbname=metatryp2_proteins ./metatryp2_db_prot.backup

3. Test that the database was successfully built by listing all the taxa in the Genomes data category. (Schema to support the data categories Specialized Assemblies and Meta-omic Assemblies is also loaded into metatryp2_proteins; however, there is no pre-loaded sequence or taxonomic data for these data types.

./bin/list_taxons.sh

4. Can now query these genomes, or add to this database by following instructions in Quick Usage Guide.

Taxa in the pre-built tutorial database:

• Full taxonomic lineages can be found here.
• Taxa listed below:
  • Aciduliprofundum boonei T469
  • Alcanivorax sp. DG881
  • Algoriphagus machipongonensis PR1
  • Alphaproteobacteria sp. SAR11 HIMB5
  • Alteromonas australica H17
  • Alteromonas macleodii Black Sea 11
  • Alteromonas macleodii D7
  • Alteromonas macleodii DE
  • Alteromonas macleodii HOT1A3
  • Alteromonas macleodii MIT1002
  • Alteromonas macleodii REDSEA-S09_B2
  • Alteromonas macleodii REDSEA-S12_B5
  • Alteromonas macleodii REDSEA-S15_B11
  • Alteromonas mediterranea DE
  • Alteromonas sp. ALT199
  • Bacillus sp. B14905
  • Bacillus sp. NRRL B-14911
  • Bacillus sp. SG-1
  • Beggiatoa sp. Orange Guaymas
  • Brevundimonas sp. BAL3
  • Caminibacter mediatlanticus TB-2
  • Candidatus Nitrosopelagicus brevis CN25
  • Candidatus Pelagibacter ubique SAR11 HTCC1062
  • Carnobacterium sp. AT7
  • Citreicella sp. SE45
  • Congregibacter litoralis KT71
  • Crocosphaera watsonii WH 0003
  • Crocosphaera watsonii WH 0005
  • Crocosphaera watsonii WH 0401 (draft1)
  • Crocosphaera watsonii WH 0402
  • Crocosphaera watsonii WH 8501
  • Crocosphaera watsonii WH 8502
  • Cyanobium sp. PCC 7001
  • Erythrobacter litoralis HTCC2594
  • Erythrobacter sp. NAP1
  • Erythrobacter sp. SD-21
  • Flavobacteria bacterium BAL38
  • Flavobacteria bacterium BBFL7
  • Fulvimarina pelagi HTCC2506
  • Gammaproteobacteria sp. OM60 HIMB55
  • Hydrogenivirga sp. 128-5-R1-1
  • Idiomarina baltica OS145
  • Janibacter sp. HTCC2649
  • Kordia algicida OT-1
  • Lentisphaera araneosa HTCC2155
  • Limnobacter sp. MED105
  • Loktanella sp. SE62
  • Loktanella vestfoldensis SKA53
  • marine actinobacterium PHSC20C1
  • Marinitoga piezophila KA3
  • Microbulbifer agarilyticus S89
  • Nitrobacter hamburgensis X14
  • Nitrococcus mobilis Nb-231
  • Nitrosopelagicus brevis 1
  • Nitrosopelagicus sp. REDSEA-S32_B2
  • Nitrosopumilus maritimus SCM1
  • Nitrospina sp. AB-629-B18
  • Nitrospina sp. SCGC AAA799-A02
  • Nitrospina sp. SCGC AAA799-C22
  • Nitrospira defluvii
  • Planctomycetaceae bacterium KSU-1
  • Prochlorococcus marinus MIT9312
  • Prochlorococcus sp. MIT9201
  • Prochlorococcus sp. MIT9202
  • Prochlorococcus sp. MIT9211
  • Prochlorococcus sp. MIT9215
  • Prochlorococcus sp. MIT9301
  • Prochlorococcus sp. MIT9302
  • Prochlorococcus sp. MIT9303
  • Prochlorococcus sp. MIT9311
  • Prochlorococcus sp. MIT9314
  • Prochlorococcus sp. MIT9321
  • Prochlorococcus sp. MIT9322
  • Prochlorococcus sp. MIT9401
  • Prochlorococcus sp. MIT9515
  • Prochlorococcus sp. NATL1A
  • Prochlorococcus sp. NATL2A
  • Prochlorococcus sp. SB
  • Prochlorococcus sp. SS35
  • Prochlorococcus sp. SS51
  • Prochlorococcus sp. SS52
  • Pseudoalteromonas arctica A 37-1-2
  • Pseudoalteromonas atlantica T6c
  • Pseudoalteromonas atlantica TB41
  • Pseudoalteromonas denitrificans DSM 6059
  • Pseudoalteromonas piscicida ATCC 15057
  • Pseudoalteromonas rubra ATCC 29570
  • Pseudoalteromonas rubra S2471
  • Richelia intracellularis RC01
  • Roseobacter litoralis Och 149
  • Roseobacter sp. AzwK-3b
  • Roseobacter sp. CCS2
  • Roseobacter sp. GAI101
  • Roseobacter sp. MED193
  • Roseobacter sp. SK209-2-6
  • Roseovarius nubinhibens ISM
  • Roseovarius sp. TM1035
  • Sagittula stellata E-37
  • SAR116 cluster alpha proteobacterium sp. HIMB100
  • SAR116 cluster alphaproteobacterium REDSEA-S10_B10N8
  • SAR116 cluster alphaproteobacterium REDSEA-S2_B12
  • Shewanella benthica KT99
  • Sphingomonas sp. SKA58
  • Stenotrophomonas sp. SKA14
  • Sulfitobacter sp. EE-36
  • Sulfitobacter sp. NAS-14.1
  • Sulfurospirillum sp. Am-N (draft)
  • Synechococcus elongatus PCC 6301
  • Synechococcus elongatus PCC 7942
  • Synechococcus sp. 7002
  • Synechococcus sp. BL107
  • Synechococcus sp. CB0101
  • Synechococcus sp. CB0205
  • Synechococcus sp. CC9311
  • Synechococcus sp. CC9605
  • Synechococcus sp. CC9616
  • Synechococcus sp. CC9902
  • Synechococcus sp. PCC 7336
  • Synechococcus sp. RS9916
  • Synechococcus sp. RS9917
  • Synechococcus sp. WH 8016
  • Synechococcus sp. WH 8109
  • Synechococcus sp. WH5701
  • Synechococcus sp. WH7803
  • Synechococcus sp. WH7805
  • Synechococcus sp. WH8102
  • Thalassobium sp. R2A62
  • Thermococcus sp. AM4
  • Trichodesmium erythraeum IMS101
  • Trichodesmium thiebautii H9-4
  • Vibrio alginolyticus 12G01
  • Vibrio campbellii AND4
  • Vibrio fischeri MJ11
  • Vibrio parahaemolyticus 16
  • Vibrio sp. MED222
  • Vibrio splendidus 12B01