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MIT License | ||
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Copyright (c) 2022 Michael Lazear | ||
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Permission is hereby granted, free of charge, to any person obtaining a copy | ||
of this software and associated documentation files (the "Software"), to deal | ||
in the Software without restriction, including without limitation the rights | ||
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
copies of the Software, and to permit persons to whom the Software is | ||
furnished to do so, subject to the following conditions: | ||
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The above copyright notice and this permission notice shall be included in all | ||
copies or substantial portions of the Software. | ||
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | ||
SOFTWARE. |
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<img src="figures/logo.png" width="300"> | ||
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# Sage: proteomics searching so fast it seems like magic | ||
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[![Rust](https://github.com/lazear/sage/actions/workflows/rust.yml/badge.svg)](https://github.com/lazear/sage/actions/workflows/rust.yml) [![Anaconda-Server Badge](https://anaconda.org/bioconda/sage-proteomics/badges/version.svg)](https://anaconda.org/bioconda/sage-proteomics) | ||
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For more information please read [the online documentation!](https://sage-docs.vercel.app/docs) | ||
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# Introduction | ||
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Sage is, at it's core, a proteomics database search engine - | ||
a tool that transforms raw mass spectra from proteomics experiments into peptide identifications | ||
via database searching & spectral matching. | ||
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However, Sage includes a variety of advanced features that make it a one-stop shop: retention time prediction, quantification (both isobaric & LFQ), peptide-spectrum match rescoring, and FDR control. You can directly use results from Sage without needing to use other tools for these tasks. | ||
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Additionally, Sage was designed with cloud computing in mind - massively parallel processing and the ability to directly stream compressed mass spectrometry data to/from AWS S3 enables unprecedented search speeds with minimal cost. | ||
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Sage also runs just as well reading local files from your Mac/PC/Linux device! | ||
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## Why use Sage instead of other tools? | ||
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Sage is **simple to configure**, **powerful** and **flexible**. | ||
It also happens to be well-tested, **mind-boggingly fast**, open-source (MIT-licensed) and free. | ||
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## Features | ||
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- Incredible performance out of the box | ||
- [Effortlessly cross-platform](https://sage-docs.vercel.app/docs/started#download-the-latest-binary-release) (Linux/MacOS/Windows), effortlessly parallel (uses all of your CPU cores) | ||
- [Fragment indexing strategy](https://sage-docs.vercel.app/docs/how_it_works) allows for blazing fast narrow and open searches (> 500 Da precursor tolerance) | ||
- [Isobaric quantification](https://sage-docs.vercel.app/docs/how_it_works#tmt-based) (MS2/MS3-TMT, or custom reporter ions) | ||
- [Label-free quantification](https://sage-docs.vercel.app/docs/how_it_works#label-free): consider all charge states & isotopologues *a la* FlashLFQ | ||
- Capable of searching for [chimeric/co-fragmenting spectra](https://sage-docs.vercel.app/docs/configuration/additional) | ||
- Wide-window (dynamic precursor tolerance) search mode - [enables WWA/PRM/DIA searches](https://sage-docs.vercel.app/docs/configuration/tolerance#wide-window-mode) | ||
- Retention time prediction models fit to each LC/MS run | ||
- [PSM rescoring](https://sage-docs.vercel.app/docs/how_it_works#machine-learning-for-psm-rescoring) using built-in linear discriminant analysis (LDA) | ||
- PEP calculation using a non-parametric model (KDE) | ||
- FDR calculation using target-decoy competition and picked-peptide & picked-protein approaches | ||
- Percolator/Mokapot [compatible output](https://sage-docs.vercel.app/docs/configuration#env) | ||
- Configuration by [JSON file](https://sage-docs.vercel.app/docs/configuration#file) | ||
- Built-in support for reading gzipped-mzML files | ||
- Support for reading/writing directly from [AWS S3](https://sage-docs.vercel.app/docs/configuration/aws) | ||
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<!-- <img src="figures/TMT_Panel.png" width="800"> --> | ||
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Check out the [blog post introducing Sage](https://lazear.github.io/sage/) for more information and full benchmarks! |
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