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kwrodarmer edited this page Jun 20, 2018 · 17 revisions

Welcome to the sra-tools wiki!

ANNOUNCEMENT:

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.

ATTENTION:

sra-tools has transitioned to all HTTPS access as of October 7, 2016 with release 2.8.0. It is critically important that you update all of your binaries and your configuration files.

This is in response to OMB memorandum M-15-13 issued on June 8, 2015, requiring all Federal HTTP servers to stop using (simple) HTTP and switch to HTTPS.

Please update your software as soon possible to give some time to ensure continued operation.

Proxy users take note - this complicates proxy usage somewhat. We will create a Wiki page dedicated to supported proxy configuration and firewall settings to help users during the conversion.

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