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1. CassisCassisPublic

   Detection and refinment of genomic rearrangement breakpoints

   Perl 1

2. SandraLouise/SVJedi-graphSandraLouise/SVJedi-graphPublic

   SV genotyper for long reads with a variation graph

   Python 12

3. GATB/MindTheGapGATB/MindTheGapPublic

   MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

   C++ 37 12

4. GATB/simkaGATB/simkaPublic

   Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.

   C++ 47 10

5. GATB/DiscoSnpGATB/DiscoSnpPublic

   DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.

   Python 38 20

6. anne-gcd/MTG-Linkanne-gcd/MTG-LinkPublic

   MTG-Link: Local assembly tool for linked-read data

   Python 3 1