| Repository or tool source | Data transfer integrity checks in place |
|---|---|
| ENA | MD5sum available for “most” downloads. Submission tool generates this, otherwise user needs to upload “Common Run Submission Errors” |
| NCBI GEO | MD5 “recommended” for submissions “Submitting High-Throughput Sequence Data to GEO” |
| NCBI SRA | MD5 is a parameter during submission (as of the 2010 guide “SRA Submission Quick Start Guide”) There is a ‘vdb-validate’ tool for checking download integrity “SRA-Tools” |
| MGnify | “Intermediate checksums” in MGnify: the microbiome analysis resource in 2020 (Mitchell et al. (2020)) |
| MG RAST | “Data hygiene” (Preprocessing, dereplication, DRISEE, screening) (Meyer et al. (2008)) |
| Comments/questions: |
|---|
| File type | Integrity check | Other considerations for quality and transferability |
|---|---|---|
| FASTQ | Read count, checksum (MD5sum, SEGUID (Bassi and Gonzalez (2007)), (Babnigg and Giometti (2006)), etc.) | Determination of +33/+64 format from compressed files |
| FASTA | Read count, checksum (MD5sum, SEGUID (Bassi and Gonzalez (2007)), (Babnigg and Giometti (2006), etc.) | |
| .faa | SEGUID (Bassi and Gonzalez (2007)), (Babnigg and Giometti (2006) | Annotation pipeline, assembly quality |
| GFF/GTF | Annotation pipeline, assembly quality |
| Comments/questions: |
|---|
Babnigg, G., and C. S. Giometti. 2006. “A Database of Unique Protein Sequence Identifiers for Proteome Studies.” Proteomics 6: 4514–22. https://doi.org/10.1002/pmic.200600032.
Bassi, S., and V. Gonzalez. 2007. “New Checksum Functions for Biopython.” Nat Prec. https://doi.org/10.1038/npre.2007.278.1.
“Common Run Submission Errors.” https://ena-docs.readthedocs.io/en/latest/faq/runs.html.
Meyer, F., D. Paarmann, M. D’Souza, R. Olson, E. M. Glass, M. Kubal, T. Paczian, et al. 2008. “The Metagenomics RAST Server — a Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes.” BMC Bioinformatics 9: 386. https://help.mg-rast.org/user_manual.html#data-hygiene.
Mitchell, Alex L, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, et al. 2020. “MGnify: The Microbiome Analysis Resource in 2020.” Nucleic Acids Research 48 (D1): D570–78. https://doi.org/10.1093/nar/gkz1035.
“SRA Submission Quick Start Guide.” https://anonsvn.ncbi.nlm.nih.gov/repos/v1/trunk/sra/doc/SRA_1-1/SRA_Quick_Start_Guide.pdf.
“SRA-Tools.” https://github.com/ncbi/sra-tools/tree/master.
“Submitting High-Throughput Sequence Data to GEO.” https://www.ncbi.nlm.nih.gov/geo/info/seq.html.