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Top 17 sequencing Open-Source Projects
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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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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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fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
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mixcr
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
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mercury
A minimal and human-readable language and environment for the live coding of algorithmic electronic music. (by tmhglnd)
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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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hgvs
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
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nextclade
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
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DNAnalyzer
Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools
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covid-19-signal
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
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Project mention: Look over my purchase, is there anything I should return? | /r/buildapc | 2023-05-06
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.
Maybe it would help you to look at the galaxy project: GitHub main site
Project mention: Calculating Average Coverage or Read Depth for a Sequence (WES) | /r/bioinformatics | 2023-06-24
Project mention: Why does musl make my Rust code so slow? (2020) | news.ycombinator.com | 2023-12-12
P.S. If you haven't checked out my latest project, DNAnalyzer, please do so! It's a groundbreaking open source tool that brings the power of machine learning to DNA analysis. You can find it on GitHub or read more about it here on dev.to. I would love to hear your feedback and suggestions on how to make it better and more useful for everyone.
xHLA on GitHub worked for me running it directly on the Nebula cram file with no additional processing. Results match those from OptiType (which had high memory requirements, was much slower and only covered 3 of the 6 common genes).
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).
sequencing related posts
- BIOINFORMATICS PROJECT
- Any bioinfo open source projects looking for contributors?
- Show HN: 16s rRNA Sequencing Meta-Analysis Reconstruction Tool
- 16SMaRT - A 16s rRNA Sequencing Meta-analysis Reconstruction Tool.
- miRDeep2_core_algorithm.pl error
- Developed a new kind of dual extruder system on fully custom built 3D printer
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A note from our sponsor - SaaSHub
www.saashub.com | 29 Apr 2024
Index
What are some of the best open-source sequencing projects? This list will help you:
| Project | Stars | |
|---|---|---|
| 1 | deepvariant | 3,076 |
| 2 | OTTO | 2,619 |
| 3 | fastp | 1,768 |
| 4 | galaxy | 1,313 |
| 5 | mosdepth | 654 |
| 6 | mixcr | 309 |
| 7 | mercury | 271 |
| 8 | hgvs | 231 |
| 9 | nextclade | 199 |
| 10 | ariba | 154 |
| 11 | GenomicSQLite | 152 |
| 12 | mirdeep2 | 130 |
| 13 | DNAnalyzer | 123 |
| 14 | HLA | 94 |
| 15 | deML | 45 |
| 16 | covid-19-signal | 30 |
| 17 | 16SMaRT | 7 |
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