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1. philres/ngmlr philres/ngmlr Public

   NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

   C++ 293 40

2. Cibiv/NextGenMap Cibiv/NextGenMap Public

   NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. This allows …

   C++ 86 8

3. Sniffles Sniffles Public

   Structural variation caller using third generation sequencing

   Python 562 95

4. schatzlab/genomescope schatzlab/genomescope Public

   Fast genome analysis from unassembled short reads

   JavaScript 261 56

5. SURVIVOR SURVIVOR Public

   Toolset for SV simulation, comparison and filtering

   C++ 358 46

6. Cibiv/Teaser Cibiv/Teaser Public

   A tool to benchmark mappers and different parameters within minutes

   HTML 43 10