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Welcome to the sra-tools wiki!
NIH has released a request for information (RFI) to solicit community feedback on new proposed Sequence Read Archive (SRA) data formats. Learn more and share your thoughts at https://go.usa.gov/xvhdr. The response deadline is July 17th, 2020. We’d encourage you all to share with your colleagues and networks, and respond if you are an SRA submitter or data user.
SRA Toolkit 2.11.1 August 17, 2021
align, axf, sra-pileup, vdb, vfs: resolve reference sequences within output directory cloud, kns, sra-tools: do not acquire CE more often than necessary kget: renamed to vdb-get kns, sra-tools: improved reporting of peer certificate information kns, sra-tools: improved timeout management in CacheTeeFile ncbi-vdb, ngs, ngs-tools, sra-tools: configure prints the version of compiler prefetch: better control of reference sequences prefetch: fixed failure when protected repository exists prefetch, vdb, vfs: prefetch with "-O" will now correctly place references in output directory prefetch, vfs: fixed error message 'multiple response SRR URLs for the same service...' when downloading prefetch: will download any missed dependencies prefetch: will not hang when failing to download dependencies sratools: allow driver tool to handle debug output for modules vdb-dump: using --info with URLs now works correctly vfs, sra-tools: updated interaction with SRA Data Locator
With release 2.9.1 of sra-tools we have finally made available the tool fasterq-dump, a replacement for the much older fastq-dump tool. As its name implies, it runs faster, and is better suited for large-scale conversion of SRA objects into FASTQ files that are common on sites with enough disk space for temporary files. fasterq-dump is multi-threaded and performs bulk joins in a way that improves performance as compared to fastq-dump, which performs joins on a per-record basis (and is single-threaded).
fastq-dump is still supported as it handles more corner cases than fasterq-dump, but it is likely to be deprecated in the future.
You can get more information about fasterq-dump in this Wiki at https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump.