seqkit
sage
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seqkit
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A look at the Mojo language for bioinformatics
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
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Help with understanding awk code
You could also check out tools specialized for FASTA processing like https://github.com/shenwei356/seqkit and https://github.com/lh3/seqtk
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What are some good examples of well-engineered bioinformatics pipelines?
Seqkit - thoroughly maintained with extensive tutorials and benchmarking info - https://github.com/shenwei356/seqkit
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
What are some alternatives?
seqtk - Toolkit for processing sequences in FASTA/Q formats
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
rush - A cross-platform command-line tool for executing jobs in parallel
fasten - :construction_worker: Fasten toolkit, for streaming operations on fastq files
mokapot - Fast and flexible semi-supervised learning for peptide detection in Python
juicer - A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
spades - SPAdes Genome Assembler
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.
fasql - DuckDB Extension for reading and writing FASTA and FASTQ Files
alphapept - A modular, python-based framework for mass spectrometry. Powered by nbdev.