Skip to content

Commit

Permalink
update Sage to 0.14.1
Browse files Browse the repository at this point in the history
  • Loading branch information
timosachsenberg authored and timosachsenberg committed Sep 22, 2023
1 parent a3e6ffb commit e492568
Show file tree
Hide file tree
Showing 10 changed files with 412 additions and 772 deletions.
284 changes: 28 additions & 256 deletions Linux/64bit/Sage/README.md

Large diffs are not rendered by default.

Binary file modified Linux/64bit/Sage/sage
Binary file not shown.
284 changes: 28 additions & 256 deletions MacOS/64bit/Sage/README.md

Large diffs are not rendered by default.

Binary file modified MacOS/64bit/Sage/sage
Binary file not shown.
21 changes: 21 additions & 0 deletions MacOS/aarch64/Sage/LICENSE
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
MIT License

Copyright (c) 2022 Michael Lazear

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:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

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.
49 changes: 49 additions & 0 deletions MacOS/aarch64/Sage/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,49 @@
<img src="figures/logo.png" width="300">

# Sage: proteomics searching so fast it seems like magic

[![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)


For more information please read [the online documentation!](https://sage-docs.vercel.app/docs)


# Introduction

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.

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.

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.

Sage also runs just as well reading local files from your Mac/PC/Linux device!

## Why use Sage instead of other tools?

Sage is **simple to configure**, **powerful** and **flexible**.
It also happens to be well-tested, **mind-boggingly fast**, open-source (MIT-licensed) and free.

## Features

- 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)


<!-- <img src="figures/TMT_Panel.png" width="800"> -->

Check out the [blog post introducing Sage](https://lazear.github.io/sage/) for more information and full benchmarks!
Binary file added MacOS/aarch64/Sage/sage
Binary file not shown.
Loading

0 comments on commit e492568

Please sign in to comment.