Alternatives and similar repositories for gatk-sv

Users that are interested in gatk-sv are comparing it to the libraries listed below

• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆285Updated 3 months ago
• abyzovlab / CNVpytor
  a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
  ☆210Updated 4 months ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆175Updated last year
• epi2me-labs / wf-human-variation
  ☆149Updated last week
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆165Updated 2 years ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆207Updated 4 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆201Updated 2 years ago
• Illumina / Nirvana
  The nimble & robust variant annotator
  ☆190Updated last year
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆139Updated 4 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆251Updated 4 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆230Updated 6 months ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆280Updated 8 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆250Updated this week
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆246Updated this week
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆202Updated last month
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆142Updated 3 years ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆285Updated last year
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆323Updated 4 years ago
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆161Updated 11 months ago
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆137Updated 3 years ago
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆237Updated last year
• Illumina / ExpansionHunter
  A tool for estimating repeat sizes
  ☆205Updated 2 years ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆173Updated 2 years ago
• novoalab / EpiNano
  Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
  ☆118Updated 6 months ago
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆131Updated 3 years ago
• gatk-workflows / gatk4-data-processing
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  ☆160Updated 3 years ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆118Updated 6 years ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆202Updated this week
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆210Updated last week