Alternatives and similar repositories for lumpy-sv:

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

• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆244Updated last week
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆540Updated 8 months ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆248Updated 9 months ago
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆374Updated last year
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆346Updated 2 weeks ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆156Updated last year
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆209Updated 4 years ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆201Updated 4 years ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆267Updated last year
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆215Updated 3 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆194Updated last year
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆314Updated 3 years ago
• akdemirlab / HiCPlotter
  “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau
  ☆184Updated 4 years ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆250Updated last year
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆248Updated 2 weeks ago
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆122Updated 3 years ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆246Updated last week
• philres / ngmlr
  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 r…
  ☆297Updated last year
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆128Updated 4 years ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆150Updated 2 years ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆208Updated 3 weeks ago
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆316Updated 2 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆196Updated 3 years ago
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆197Updated this week
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆307Updated last week
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆310Updated 9 months ago
• Illumina / ExpansionHunter
  A tool for estimating repeat sizes
  ☆191Updated last year
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆267Updated last month
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆265Updated last year
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆319Updated last year