#1
A fast and sensitive gapped read aligner
794 starsJun 1, 2026 pushgeo-scienceC++Bioinformatics
$ npx skills add BenLangmead/bowtie2Alternatives
Salmon alternatives for AI agents.
Compare similar skills by workflow fit, trust score, quality, GitHub adoption, maintenance, and install readiness.
Current skill
Salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
87
Quality
88
Trust
893
Stars
#2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
753 starsJun 15, 2026 pushgeo-sciencePythonBioinformatics
$ npx skills add scverse/PyDESeq2#3
Official git repository for Biopython (originally converted from CVS)
5.1K starsJun 8, 2026 pushgeo-sciencePythonBioinformatics
$ npx skills add biopython/biopython#4
A DSL for data-driven computational pipelines
3.4K starsJun 16, 2026 pushgeo-scienceGroovyBioinformatics
$ npx skills add nextflow-io/nextflow#5
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
2.4K starsJun 1, 2026 pushgeo-scienceC++Bioinformatics
$ npx skills add OpenGene/fastp#6
Making Protein folding accessible to all!
2.8K starsJun 15, 2026 pushgeo-scienceJupyter NotebookBioinformatics
$ npx skills add sokrypton/ColabFold#7
Single-cell analysis in Python. Scales to >100M cells.
2.5K starsJun 15, 2026 pushgeo-sciencePythonBioinformatics
$ npx skills add scverse/scanpy#8
MMseqs2: ultra fast and sensitive search and clustering suite
2.1K starsJun 15, 2026 pushgeo-scienceCBioinformatics
$ npx skills add soedinglab/MMseqs2#9
A versatile pairwise aligner for genomic and spliced nucleotide sequences
2.2K starsMay 19, 2026 pushgeo-scienceCBioinformatics
$ npx skills add lh3/minimap2#10
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
1.2K starsJun 8, 2026 pushgeo-sciencePythonBioinformatics
$ npx skills add scikit-bio/scikit-bio#11
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
1.6K starsJun 16, 2026 pushgeo-scienceGoBioinformatics
$ npx skills add shenwei356/seqkit#12
Conda recipes for the bioconda channel.
1.8K starsJun 16, 2026 pushgeo-scienceShellBioinformatics
$ npx skills add bioconda/bioconda-recipes#13
Official code repository for GATK versions 4 and up
2.0K starsJun 16, 2026 pushgeo-scienceJavaBioinformatics
$ npx skills add broadinstitute/gatk#14
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
1.1K starsJun 15, 2026 pushgeo-scienceScalaBioinformatics
$ npx skills add broadinstitute/cromwell#15
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
1.0K starsJun 14, 2026 pushgeo-sciencePythonBioinformatics
$ npx skills add omicverse/omicverse#16
Data intensive science for everyone.
1.8K starsJun 16, 2026 pushgeo-sciencePythonBioinformatics
$ npx skills add galaxyproject/galaxyHow to choose
When should you switch?
Use an alternative when it has a clearer install path, higher trust score, fresher maintenance, or better platform fit for your current agent stack. Keep Salmon if it already passes your workflow test and repository review.
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Compare top candidates side by side
Open the compare page, test the install commands in a sandbox, and check each repository before using a skill in production.