seqkit
juicer
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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
juicer
What are some alternatives?
seqtk - Toolkit for processing sequences in FASTA/Q formats
sage - Proteomics search & quantification so fast that it feels like magic
gatk4-genome-processing-pipeline-azure - Workflows used for processing whole genome sequence data + germline variant calling.
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.
smk-simple-slurm - A simple Snakemake profile for Slurm without --cluster-config
spades - SPAdes Genome Assembler
fasql - DuckDB Extension for reading and writing FASTA and FASTQ Files
trinityrnaseq - Trinity RNA-Seq de novo transcriptome assembly