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Welcome to the sra-tools wiki!

ANNOUNCEMENTS:

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.

2020-06-29 2.10.8 Release:

kproc, fasterq-dump: fixed problem with seg-faults caused by too small stack used by threads

kdbmeta: allow to work with remote runs

kdb, vdb, vfs, sra-tools: fixed bug preventing use of path to directory created by prefetch if it ends with '/'

vfs, sra-tools, ngs-tools: report an error when file was encrypted for a different ngc file

prefetch: print error message when cannot resolve reference sequence

vfs, prefetch: download encrypted phenotype files with encrypted extension

vdb, sra-docker: config can auto-generate LIBS/GUID when in a docker container

2020-04-02 2.10.5 Release:

build, sratools: fixed a potential build problem in libutf8proc

ncbi-vdb, ngs, ngs-tools, sra-tools: all Linux builds now use g++ 7.3 (C++11 ABI)

prefetch: improvements were made to work in environments with bad network connections

prefetch, sratools: fixed the names of the --min-size and --max-size command line arguments when running prefetch

2020-02-26 2.10.4 Release

The 2.10.4 fixed errors when using ngc file for downloading dbGaP data.

2020-02-18

The 2.10.3 releases fixed a problem resulting in a segmentation fault in the following tools: sraxf, fasterq-dump, fastq-dump, sam-dump

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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.