graph TD;
GenoHub[**GenoHub**
Demultiplexed and compressed sequence reads in FASTQ format. Files should end in “.fastq.gz” or “.fq.gz”]
Metadata[**Metadata CSV**
Information for all samples in the GenoHub project. Must include the following columns:
***ID:*** GenoHub sample name
***R1:*** read 1 FASTQ file name
***R2:*** read 2 FASTQ file name
***Taxon:*** your best guess at taxonomic assignment
***UniqID:*** unique identifier linked to a voucher/tissue sample
]
Analyses(Run quality/adapter trimming, mitogenome assembly, etc)
Scratch[(**Hydra Scratch**
/scratch/nmnh_ocean_dna
40 TB. Not backed up, no automatic file purging.)]
Store[(**Hydra Store**
/store/public/oceandna
40 TB. Not backed up, no automatic file purging. For large raw data files and inactive projects. Drive system is slower, can't be used for active analysis)]
PDrive[(**P Drive**
P:\NMNH-OCEAN-DNA
80 TB. Incrementally backed up daily, fully backed up weekly. Only accessible from SI computers.)]
Move1[download raw FASTQ files]
Move3[copy important results]
Move4[Dan M. runs monthly and on-demand backup]
Metadata-->Store
GenoHub-->Move1
Move1-->Store
Move1-->Scratch
subgraph " "
Scratch-->Analyses
Analyses-->Move3
Move3-->Store
end
Store-->Move4
Move4-->PDrive
classDef process stroke:black,color:white,fill:#159BD7,stroke-dasharray: 5 5
classDef storage stroke:black,color:white,fill:#159BD7
classDef ccr stroke:black,color:white,fill:#159BD7
class Rename,Analyses,Move1,Move2,Move3,Move4 process
class Metadata,GenoHub,Scratch,Store,PDrive storage
click Rename "bestpractices.html"
linkStyle default stroke:grey, stroke-width:4px
Data management workflow
The following is a proposed data management guide for SI Ocean DNA sequence data. This workflow was designed for genome skimming datasets, but could be adapted for other project types.
Important
Please see the README.md the Ocean DNA Hydra Store directory for details about where to upload raw data and how to name files and directories.