Alternatives and similar repositories for lumpy-sv

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

• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆317Updated 2 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆318Updated 3 years ago
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆228Updated 3 years ago
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆397Updated last year
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆274Updated 4 months ago
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆212Updated 5 years ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆257Updated last year
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆326Updated 4 months ago
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆380Updated this week
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆246Updated 3 weeks ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆486Updated last month
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆263Updated 2 weeks ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆277Updated 8 months ago
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆319Updated last week
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆275Updated 2 years ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆272Updated 3 weeks ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆163Updated 2 years ago
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆283Updated 11 months ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆351Updated 5 months ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆383Updated last month
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆205Updated 4 years ago
• Illumina / ExpansionHunter
  A tool for estimating repeat sizes
  ☆198Updated last year
• GregoryFaust / samblaster
  samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
  ☆234Updated 4 years ago
• 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…
  ☆306Updated last year
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆259Updated 2 years ago
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆429Updated 4 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆553Updated last year
• lh3 / wgsim
  Reads simulator
  ☆281Updated 4 years ago
• genome-in-a-bottle / giab_data_indexes
  This repository contains data indexes from NIST's Genome in a Bottle project.
  ☆258Updated last year