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1. vgteam/vgvgteam/vgPublic

   tools for working with genome variation graphs

   C++ 1.3k 219

2. waveygang/wfmashwaveygang/wfmashPublic

   base-accurate DNA sequence alignments using WFA and mashmap3

   C++ 222 26

3. pangenome/pggbpangenome/pggbPublic

   the pangenome graph builder

   Shell 510 50

4. pangenome/seqwishpangenome/seqwishPublic

   alignment to variation graph inducer

   Rust 163 22

5. pangenome/smoothxgpangenome/smoothxgPublic

   linearize and simplify variation graphs using blocked partial order alignment

   C++ 63 11

6. freebayes/freebayesfreebayes/freebayesPublic

   Bayesian haplotype-based genetic polymorphism discovery and genotyping.

   C++ 876 274