Top 5 Nextflow Pipeline Projects
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rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Not really sure why it's a problem for you, I'm working on rnaseq and they use a very big input dataset, also outputs huge datasets too. It uses docker so you can deploy fast on VMs.
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sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
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OPS
OPS - Build and Run Open Source Unikernels. Quickly and easily build and deploy open source unikernels in tens of seconds. Deploy in any language to any cloud.
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Project mention: Is it possible to assemble a complete bacterial genome using short reads? | reddit.com/r/bioinformatics | 2021-08-09
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So after a lot of reading and talking with some people i was able to do it with the eager pipeline (https://github.com/nf-core/eager) migth be a bit dificult to set up, but it is really useful. I leave this here for you and other people that may see this ;)
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Project mention: Ask HN: How to be my own genetic disease researcher for my partner? | news.ycombinator.com | 2021-12-06
Here's a post I made on reddit about how to do exactly this:
https://www.reddit.com/r/Nebulagenomics/comments/nhjfpa/how_...
You use the VCF and a java project called the Exomiser, and it will give you output files with all the pathogenic variants marked
In my case and is the case with a lot of rare diseases you could have unique pathology and mutations in a certain gene but that don't show up as pathogenic in clin var. For example my family has a lot of autoimmune diseases and as expected my HLA genes are totally trashed. However none of these mutations have ever been seen and flagged before especially was WGS is so new.
If you only have a list of genes and the genomizer will give you a list of the genes that are the most heaviy affected, you can put them into this app to get some further data and idea about what kind of tissue expression or rare disease spectrums you may be dealing with: https://maayanlab.cloud/Enrichr/
sadly the reality is though you can have all that and it almost puts you at a disadvatnage with doctors because you look crazy and sus claiming you have some HLA mutation or whatever. Who told you that? Oh well I data mined it...uh huh sure....honestly to get it back into the medical system and to be taken seriously you'd probably have to get a doctor to retest it, for example I can can spin this up to get my HLA alleles from my fastq https://github.com/nf-core/hlatyping
But no doctor is going to put that in my medical record until I convince them to run a blood test for the same damn thing.
if anyone wants to help me with my own genetic search woes and help me out or know solutions please let me know. if you want to help me publish or add to that guide somewhere let me know - i asked nebula if they wanted to print it on the blog and they said the'd be interested but I just never cleaned it up
Nextflow Pipeline related posts
Index
What are some of the best open-source Pipeline projects in Nextflow? This list will help you:
| Project | Stars | |
|---|---|---|
| 1 | rnaseq | 416 |
| 2 | sarek | 142 |
| 3 | mag | 76 |
| 4 | eager | 61 |
| 5 | hlatyping | 25 |
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