Alternatives and similar repositories for lumpy-sv:

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

• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆378Updated last year
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆268Updated last year
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆355Updated last week
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆246Updated last month
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆316Updated 2 years ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆375Updated last year
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆250Updated 10 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆541Updated 9 months ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• 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…
  ☆299Updated last year
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆209Updated 4 years ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆316Updated 11 months ago
• pcingola / SnpEff
  ☆272Updated 2 months ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆252Updated last month
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆196Updated 4 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆265Updated last year
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆131Updated 4 years ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆151Updated 3 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆157Updated 2 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆315Updated 3 years ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆268Updated 3 months ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆203Updated 4 years ago
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆192Updated 2 months ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆251Updated last week
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆277Updated 6 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆212Updated 3 weeks ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆253Updated last year
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆330Updated this week
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆463Updated last week
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆312Updated last month