Files Generated by the Archive
Why Are There Two Versions Of My Files?
Wherever possible ENA presents two versions of your data: the file or files you submitted, and equivalent files generated by the archive.
The submitted files are kept exactly as you provided them, so the original record is preserved. The archive-generated files are converted to a consistent format, so that anyone consuming ENA data knows what to expect and can process it without adapting to each submitter’s choices.
Both appear together in the ENA Browser, under ‘Submitted files’ and ‘Generated files’ for runs, and under ‘Analysis Files’ for analyses.
What Files Does ENA Generate For My Runs?
FASTQ files.
A paired submission produces <run_accession>_1.fastq.gz and <run_accession>_2.fastq.gz; an unpaired one
produces <run_accession>.fastq.gz.
Oxford Nanopore and PacBio consensus reads also produce a <run_accession>_consensus.fastq.gz file, and PacBio
subreads a <run_accession>_subreads.fastq.gz file.
Note, however, that generated FASTQs will not be available for the following submissions:
BAM/CRAM files containing @PG:longranger
BAM/CRAM files containing @PG:cellranger
BAM/CRAM files containing CB:Z,CR:Z,CY:Z,RX:Z,QX:Z tags
Complete Genomics native (data folder) submissions
PacBio native (HDF5) submissions
ONT native format submissions
The read headers in generated FASTQ files are rewritten to a standard form built from the run accession and the spot index, so they will not match the read names you submitted.
See Archive-generated run files for the full naming table and the read-header field definitions.
What Files Does ENA Generate For My Analyses?
FASTA files, for primary and binned metagenome assemblies. These submissions receive ERZ accessions only — no GCA assembly accession and no sequence accessions.
As with runs, the point is consistency: submitted analysis files may be FASTA, BAM, CRAM, VCF, BED or others, and the generated FASTA gives users a predictable format to work with.