genome-in-a-bottle / giab_tools_methods

This repository contains a list of tools or methods that have been used in GIAB analysis

giab_tools_methods

This repository contains a list of tools or methods that have been used in GIAB data analysis

1. RTG Tools:
   _{github: https://github.com/RealTimeGenomics/rtg-tools
   Paper: Joint variant and de novo mutation identification on pedigrees from high-throughput sequencing data.
   giab ftp: ftp://ftp-trace.ncbi.nih.gov/giab/ftp/tools/RTG/}
   

2. GATK:
   _{github: https://github.com/broadgsa/gatk/ (or https://www.broadinstitute.org/gatk/ )
   Paper: A framework for variation discovery and genotyping using next-generation DNA sequencing data}
   

3. freebayes:
   _{github: https://github.com/ekg/freebayes
   Paper: Haplotype-based variant detection from short-read sequencing}
   

4. SVClassify
   _{github: https://github.com/usnistgov/SVClassify
   Paper: svclassify: a method to establish benchmark structural variant calls}
   

5. PBHoney
   _{sourceforge: https://sourceforge.net/projects/pb-jelly/ (or https://www.hgsc.bcm.edu/software/honey)
   Paper: PBHoney: identifying genomic variants via long-read discordance and interrupted mapping}
   

6. MetaSV
   _{github: https://github.com/bioinform/metasv
   Paper: MetaSV: an accurate and integrative structural-variant caller for next generation sequencing}
   

7. ParliamentSV
   _{sourceforge: http://sourceforge.net/projects/parliamentsv
   Paper: Assessing structural variation in a personal genome — towards a human reference diploid genome}
   

8. VariationHunter
   _{sourceforge: http://variationhunter.sourceforge.net/Home
   Paper: Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery}
   

9. Jitterbug
   _{sourceforge: http://sourceforge.net/projects/jitterbug/
   Paper: Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution}
   

10. CGAtools
    _{sourceforge: http://cgatools.sourceforge.net/}
    

11. CORTEX
    _{sourceforge: http://cortexassembler.sourceforge.net/index_cortex_var.html
    Paper: http://www.ncbi.nlm.nih.gov/pubmed/22231483}
    

12. FALCON
    _{github: https://github.com/PacificBiosciences/falcon}
    

13. PBSV
    _{github: https://github.com/PacificBiosciences/pbsv}
    

14. Peregrine
    _{github: https://github.com/cschin/Peregrine}
    

15. SVanalyzer
    _{https://github.com/nhansen/SVanalyzer}