sage
alphapept
| sage | alphapept | |
|---|---|---|
| 5 | 2 | |
| 194 | 157 | |
| - | 3.2% | |
| 7.7 | 6.4 | |
| 8 days ago | 23 days ago | |
| Rust | HTML | |
| MIT License | Apache License 2.0 |
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sage
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Does anyone know a great guide/documentation explaining how to implement Percolator?
If you want to implement LDA from scratch, you could check out how Sage is doing it.
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What are some good examples of well-engineered bioinformatics pipelines?
You could check out https://github.com/lazear/sage - it's a near comprehensive program/pipeline for analyzing DDA/shotgun proteomics data. Most proteomics pipelines consist of running multiple, separate tools in sequence (search, spectrum rescoring, retention time prediction, quantification), but sage performs all of these. This cuts down on the need for disk space for storing intermediate results (none required), the need for IO (files are read once), and results in a proteomics pipeline that is >10-1000x faster than anything else, including commercial solutions
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Proteomics search engine written in Rust
You can also check out the intro blog post if you're interesting in learning more about the algorithm behind Sage. Beyond being fast, it also includes integrated machine learning (linear discriminant analysis, KDE) for rescoring spectral matches.
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Opinions on AlphaPept
You could try out Sage, if you're looking for speed - I don't think you'll find anything faster. https://github.com/lazear/sage
alphapept
What are some alternatives?
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
openchrom - Visualization and Analysis of mass spectrometric and chromatographic data.
seqkit - A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
docker-builds - :package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
fasten - :construction_worker: Fasten toolkit, for streaming operations on fastq files
mokapot - Fast and flexible semi-supervised learning for peptide detection in Python
galaxytools - Set of Galaxy tool wrappers developed at RECETOX
juicer - A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
training-material - A collection of Galaxy-related training material
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.
pypop - PyPop: Python for Population Genomics