#1
Official code repository for GATK versions 4 and up
2.0K starsJun 16, 2026 pushgeo-scienceJavaBioinformatics
$ npx skills add broadinstitute/gatkAlternatives
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Data intensive science for everyone.
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#2
Official git repository for Biopython (originally converted from CVS)
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$ npx skills add biopython/biopython#3
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$ npx skills add lindenb/jvarkit#4
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$ npx skills add hail-is/hail#5
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$ npx skills add kblin/ncbi-genome-download#6
Tools to process and analyze deep sequencing data.
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$ npx skills add deeptools/deepTools#7
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$ npx skills add danforthcenter/plantcv#8
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$ npx skills add tanghaibao/jcvi#9
A versatile pairwise aligner for genomic and spliced nucleotide sequences
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$ npx skills add lh3/minimap2#10
Conda recipes for the bioconda channel.
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$ npx skills add bioconda/bioconda-recipes#11
Single-cell analysis in Python. Scales to >100M cells.
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$ npx skills add scverse/scanpy#12
Quickly search, compare, and analyze genomic and metagenomic data sets.
547 starsJun 15, 2026 pushgeo-sciencePythonBioinformatics
$ npx skills add sourmash-bio/sourmash#13
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#14
A cross-platform command-line tool for executing jobs in parallel
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$ npx skills add shenwei356/rush#15
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
1.1K starsMar 17, 2026 pushgeo-scienceScalaBioinformatics
$ npx skills add bigdatagenomics/adam#16
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/omicverseHow 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 Galaxy if it already passes your workflow test and repository review.
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