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Are the sample accessions (ENA/SRA experiment accession) and phenotypes available?
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The current implementation of fastq-dl doesn't seem very robust to avoid downloading SRA-Lite files. One alternative is to reimplement the workflow by leveraging NCBI's Fasterq-dump directly
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I'll use this issue to document steps to build a `k=31,scaled=1000` index for SRA metagenomes. This is the same process used for the current `k=21,scaled=1000` index in branchwater.sourmash.bio, but c…
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**Community Note**
- Please vote on this issue by adding a 👍 [reaction](https://blog.github.com/2016-03-10-add-reactions-to-pull-requests-issues-and-comments/) to the original issue to help the commu…
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Does this work with SRA Lite?
https://ncbiinsights.ncbi.nlm.nih.gov/2021/10/19/sra-lite/
moqri updated
7 months ago
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Solve this error as soon as possible
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The new documentation #552 contains also a revamped tutorial. However, some important sets of functionalities miss a tutorial:
- [ ] `tantan` application interface: `tutorial/application/tantan`
-…
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- [48d354f5-a5ca-4f35-a3bb-fa3687502252](https://cellxgene.cziscience.com/collections/48d354f5-a5ca-4f35-a3bb-fa3687502252)
- obs.var_time:P7 - update to 7 day [MmusDv:0000117]
- [d86517f0-fa7e-4…
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Hi,
In "metabuli classify" commnad, is it possible to specify multiple fastqs ? (e.g. as a list)
I would like to reduce the D.B loading time for profiling thousands of SRA fastqs.
Best,
K…
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This code
```console
nextflow run fmalmeida/ngs-preprocess -r dev -latest -profile docker --sra_ids "./input/sra_ids.txt" --output illumina_single --shortreads_type "single" --fastp_addit…