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Sra-tools Alternatives
Similar projects and alternatives to sra-tools
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WorkOS
The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a better sra-tools alternative or higher similarity.
sra-tools reviews and mentions
Posts with mentions or reviews of sra-tools.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-10-10.
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Bulk RNA seq analysis.
Note that conda sra-tools does not support ARM (M chips use customized ARM architecture ) yet and the official repo also does not provide pre-compiled version for arm. You should be able to compile it from the source but YMMV. Similarly, STAR does not officially support ARM either but compilation on your own always worths a try.
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fasterq-dump target disk-limit
According to this, the disk space required should be about 17 times the size of the accession (for both output files and tmp files). As can be seen below, I have >500GB of disk space. Yet, I receive this output:
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Scientists Are Finding Fungi in Cancerous Tumors
Start with downloading SRA toolkit: https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-To...
Find some data of interest: https://www.ncbi.nlm.nih.gov/sra?term=(%22Homo%20sapiens%22[... (This searches SRA for human genome sequences on illumina with fastq files available)
Run fasterq-dump on the SRR (listed as "Runs" in the SRA page of your choice):
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Systematic way to collect GEO datasets
If you are okay with looking at already processed data, chdck out https://dee2.io/. Otherwise there is https://github.com/ncbi/sra-tools for getting fastq files (a cli tool) or https://github.com/saketkc/pysradb (python)
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How to extract gene sequences from SRA
Fasterq-dump also doesnt play nice sometimes. By that I mean it causes problems like this https://github.com/ncbi/sra-tools/issues/383
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How do I enable prefetch? Keep getting "-bash: defaults: command not found"
In this case, you're missing software. Specifically, you're missing sra-tools. Fortunately, this is provided via Homebrew as sratoolkit. After installing that formula, you should be able to use the prefetch command.
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SRAToolKit for pipeline
Yeah, unfortunately this required key entry is by design for some reason (see more here https://github.com/ncbi/sra-tools/issues/291).
- SRA data from NCBI - moved?
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A note from our sponsor - WorkOS
workos.com | 29 Apr 2024
Stats
Basic sra-tools repo stats
8
1,049
9.2
7 days ago
ncbi/sra-tools is an open source project licensed under GNU General Public License v3.0 or later which is an OSI approved license.
The primary programming language of sra-tools is C.
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