seqkit
biogo
seqkit | biogo | |
---|---|---|
3 | 3 | |
1,205 | 368 | |
- | 0.0% | |
8.5 | 0.0 | |
6 days ago | almost 2 years ago | |
Go | Go | |
MIT License | BSD 3-clause "New" or "Revised" License |
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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
biogo
-
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
-
How is GO used in bioinfo?
There is bĂogo which is a general genomics library (dealing with file parsing, mostly) in the vein of Bioperl, BioPython and the other Bio* libraries. I've not really ever used it though - I almost used it the other day but the BAM parser was too bare bones for my purposes so I opted to do what I wanted in Python.
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So I evaluated Go for my next project and liked it, but ultimately didn't choose it
Btw, there is a bioinformatics scene in Go: https://github.com/biogo/biogo
What are some alternatives?
seqtk - Toolkit for processing sequences in FASTA/Q formats
sage - Proteomics search & quantification so fast that it feels like magic
rush - A cross-platform command-line tool for executing jobs in parallel
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
juicer - A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
spades - SPAdes Genome Assembler
fasql - DuckDB Extension for reading and writing FASTA and FASTQ Files
gatk4-genome-processing-pipeline-azure - Workflows used for processing whole genome sequence data + germline variant calling.