seqkit
rush
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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
rush
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Design of GNU Parallel
If anyone needs a pretty basic alternative with Windows support, there's Rush:
https://github.com/shenwei356/rush
I use it pretty extensively with ffmpeg, imagemagick and the like.
I'd been using the mmstick/parallel for a while, but it moved to RedoxOS repos and then stopped being updated, while still having some issues not ironed out.
https://github.com/shenwei356/rush
What are some alternatives?
seqtk - Toolkit for processing sequences in FASTA/Q formats
gnu_parallel
sage - Proteomics search & quantification so fast that it feels like magic
tpack - Pack a Go workflow/function as a Unix-style pipeline command
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.