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The get-geo-annotations.R script here:
https://github.com/Sage-Bionetworks/syndccutils/blob/master/R/scripts/get-geo-annotations.R
extracts links on a per-sample/per-file basis to BioSample. e.g.,…
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This Python module seems to be a reasonably easy-to-use and portable way to slurp a stream of reads from the SRA: https://github.com/ncbi/ngs/tree/master/ngs-python.
It depends on a library that they…
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Page is started here, needs more work: https://galaxyproject.org/support/ncbi-sra-fastq/
Ideas:
- Cover both BAM and Fastq manipulation/prep?
- Add highlights from a tutorial that covers this a…
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I tried to use prefetch from SRA Toolkit to extract raw sequence data in fastq format from SRA
##prefetch -v SRR10509508
##prefetch SRR10509508
###########
But Prefetch was giving the following er…
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In the SRA db, in the run info, as well as in the XML, one can see variables such as "GISAID_Accession" and "SARS-CoV-2_diagnostic_pcr_Ct_value_1" for certain samples (below).
https://www.ncbi.nlm.…
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The MiAIRR SRA element field for Sequencing Platform is not right, its example is for an instrument model and the Sequencing Platform should have a short list (about 8) of the platforms in a checklist…
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## User story
>As a curator
>I want to be able to add accession numbers of externally hosted linked data
>So that we can link directly to relevant data hosted in external repositories such as INS…
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associated with: http://ivory.idyll.org/blog/2017-sourmash-sra-microbial-wgs.html
see https://github.com/dib-lab/soursigs/blob/3db6162579e0efbc4fe8f181a7f08c3aee391d97/Snakefile#L149
```
http:/…
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https://pypi.org/project/lat-lon-parser/
#4 fixed variable name when normalizing metadata, but we are still missing lat/lon combinations in the values because it is a freeform text field...
(tha…
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I have installed `sra-tools` v3.0.10 distributed from Bioconda for **linux-64** platform. Running `fasterq-dump` occupies far more RAM than the flags would imply (default 100 MB/core) or I have ever e…