2016-09-28: HTTP(s) Access to SRA Has Been Restored more...less...
Service was restored at approximately 3:40 PM EDT.
Starting on or about September 28th 2016 at 2:00 PM EDT, NCBI network services and the SRA began to fail and are either sporadically working or completely unavailable.
Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Pond-221812' containing sample 'Escherichia coli HVH 199 (4-5670322)'(SRR784607)
|Run||Spots||Bases||Size||GC content||Published||Access Type|
This run has 2 reads per spot:
|L=101, 100%||L=101, 100%|
Technical read Application Read L=4, 100% Length is 4, 100% spots contain this read ̅L=165, σ=92.8, 66% Average length is 165, standard deviation is 92.8, 66% spots contain this read
|base caller||2013-03-08 22:34:25.0||GAPipeline||RTA22.214.171.124||Sequencer Application 126.96.36.199|
SRA Toolkit tools directly operate on SRA runs. Toolkit has capacity to find requested runs at NCBI and download (and cache) only the part you really need. For example quality scores represent a majority of data volume and you may not need them if you dump fasta only (versus fastq). Or if you are looking at particular gene you may not need the reads aligned to other regions or not aligned at all.
If you plan to run data analysis in environment where getting data from NCBI at run time is unfeasible you can use SRA Toolkit prefetch utility to cache all data in advance. Read more at SRA Knowledge Base on how to download SRA data using command line utilities.
Please use SRA Run Selector to filter and download list of SRA runs in the scope of experiment, sample or study.
In addition to it you can download the following data:
Taxonomy Analysis (alpha)
- experimental and error prone
- still short on documentation
- reference genomes are derived from refseq_genome blast database (which we do no claim to be perfect)
- uses 32-mers as base of comparision