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Top 23 Bioinformatic Open-Source Projects
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InfluxDB
Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
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deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
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awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
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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.
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fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
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Rust-Bio
This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.
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deep_gcns_torch
Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org
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getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
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course Computer science is very wast field the fundamental remains same, learn basic fundamentals, data structures, concepts of object oriented programming.
Project mention: Look over my purchase, is there anything I should return? | /r/buildapc | 2023-05-06
> It's been a while since you can rerun/resume Nextflow pipelines
Yes, you can resume, but you need your whole upstream DAG to be present. Snakemake can rerun a job when only the dependencies of that job are present, which allows to neatly manage the disk usage, or archive an intermediate state of a project and rerun things from there.
> and yes, you can have dry runs in Nextflow
You have stubs, which really isn't the same thing.
> I have no idea what you're referring to with the 'arbitrary limit of 1000 parallel jobs' though
I was referring to this issue: https://github.com/nextflow-io/nextflow/issues/1871. Except, the discussion doesn't give the issue a full justice. Nextflow spans each job in a separate thread, and when it tries to span 1000+ condor jobs it die with a cryptic error message. The option of -Dnxf.pool.type=sync and -Dnxf.pool.maxThreads=N prevents the ability to resume and attempts to rerun the pipeline.
> As for deleting temporary files, there are features that allow you to do a few things related to that, and other features being implemented.
There are some hacks for this - but nothing I would feel safe to integrate into a production tool. They are implementing something - you're right - and it's been the case for several years now, so we'll see.
Snakemake has all that out of the box.
fastp + multiQC + Salmon + DESeq2 all some nextflow workflow. It is a good exercise (not complicated) to create the pipeline from scratch the first time to properly understand each tool.
Project mention: Ask HN: Comment here about whatever you're passionate about at the moment | news.ycombinator.com | 2023-11-06Interested as well! But the future is not so dark, things like e.g. https://github.com/lh3/minimap2 are a breath of fresh air.
Project mention: my friend showed me his code, thees are all functions | /r/ProgrammerHumor | 2023-05-25Check out these sweet macros (from the same repo): https://github.com/lh3/bwa/blob/139f68fc4c3747813783a488aef2adc86626b01b/kbtree.h
Maybe it would help you to look at the galaxy project: GitHub main site
seqtk: A lightweight and versatile tool for processing FASTQ and FASTA files. https://github.com/lh3/seqtk
I've been thinking to learn Rust for these use cases, but always get frustrated with the complexity.
I find Go is a great middle-ground though! And now there starts to be a few more bio-related tools and toolkits out there, including:
- https://github.com/vertgenlab/gonomics
- https://github.com/biogo/biogo
- https://github.com/shenwei356/bio
... except from there being some really popular bio tools written in Go, like:
- https://github.com/shenwei356/seqkit
fastp + multiQC + Salmon + DESeq2 all some nextflow workflow. It is a good exercise (not complicated) to create the pipeline from scratch the first time to properly understand each tool.
NOTE:
The open source projects on this list are ordered by number of github stars.
The number of mentions indicates repo mentiontions in the last 12 Months or
since we started tracking (Dec 2020).
Bioinformatics related posts
- Bioawk: Awk Modified for Biological Data
- A look at the Mojo language for bioinformatics
- Outperforming Rust DNA sequence parsing benchmarks by 50% with Mojo
- R pipelines for bulk RNA-seq analyses
- Ask HN: Comment here about whatever you're passionate about at the moment
- NHI Genome Studies: Mexico Govt Sept 12 Congressional hearing
- Bioinformatics Data Structures in Rust
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A note from our sponsor - SaaSHub
www.saashub.com | 24 Apr 2024
Index
What are some of the best open-source Bioinformatic projects? This list will help you:
| Project | Stars | |
|---|---|---|
| 1 | cs-video-courses | 64,788 |
| 2 | dash | 20,472 |
| 3 | Biopython | 4,158 |
| 4 | deepvariant | 3,076 |
| 5 | awesome-single-cell | 2,898 |
| 6 | Awesome-Bioinformatics | 2,874 |
| 7 | nextflow | 2,538 |
| 8 | fastp | 1,760 |
| 9 | scanpy | 1,745 |
| 10 | minimap2 | 1,684 |
| 11 | scispacy | 1,612 |
| 12 | bioconda-recipes | 1,565 |
| 13 | Rust-Bio | 1,494 |
| 14 | bwa | 1,443 |
| 15 | galaxy | 1,313 |
| 16 | seqtk | 1,308 |
| 17 | MMseqs2 | 1,246 |
| 18 | seqkit | 1,202 |
| 19 | MultiQC | 1,161 |
| 20 | deep_gcns_torch | 1,104 |
| 21 | getting-started-with-genomics-tools-and-resources | 1,058 |
| 22 | scipipe | 1,054 |
| 23 | react-plotly.js | 990 |
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