Alternatives and similar repositories for GeneVar

Users that are interested in GeneVar are comparing it to the libraries listed below

• jmonlong / sveval
  Functions to compare a SV call sets against a truth set.
  ☆30Updated 7 months ago
• ACEnglish / usable_vcf
  Run multiple programs to check if a VCF is usable
  ☆11Updated 5 years ago
• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 4 years ago
• aganezov / RCK
  RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes
  ☆18Updated 5 years ago
• collaborativebioinformatics / STRdust
  ☆13Updated 3 years ago
• Magdoll / CoSA
  Coronavirus (SARS-Cov-2) sequencing analysis
  ☆10Updated 4 years ago
• brentp / tnsv
  add true-negative SVs from a population callset to a truth-set.
  ☆15Updated 3 years ago
• kehrlab / PopIns2
  Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
  ☆26Updated last year
• zhixingfeng / iGDA
  Detect and phase minor SNVs from long-read sequencing data
  ☆14Updated 4 years ago
• ChaissonLab / hmcnc
  Hidden Markov Model based Copy number caller
  ☆20Updated 2 months ago
• edawson / svaha2
  Linear-time, low-memory construction of variation graphs
  ☆20Updated 6 years ago
• Parsoa / Nebula
  Ultra-efficient mapping-free structural variation genotyper
  ☆20Updated 4 years ago
• sinamajidian / phaseme
  A tool set to assess the quality of the per read phasing and reduce the errors.
  ☆13Updated 5 years ago
• mcfrith / dnarrange
  ☆16Updated last year
• wdecoster / surpyvor
  A python wrapper around SURVIVOR
  ☆20Updated last year
• WHops / NAHRwhals
  R package and wrapper functions for identifying serial structural variations from genome assemblies
  ☆29Updated last year
• kcleal / svbench
  Benchmark structural variant calls against a reference set
  ☆18Updated last week
• kehrlab / PopDel
  Population-wide Deletion Calling
  ☆35Updated 9 months ago
• ekg / pafcheck
  PAF (pairwise alignment format) validator based on extended CIGAR strings
  ☆15Updated 5 months ago
• jbelyeu / unfazed
  Unfazed by genomic variant phasing
  ☆27Updated last year
• TNTurnerLab / HAT
  HAT is a set of tools for calling de novo variants from whole-genome sequencing data.
  ☆24Updated 2 months ago
• luntergroup / bamsplit
  Split a BAM file by haplotype support
  ☆16Updated 8 years ago
• langmead-lab / reference_flow
  Reducing reference bias using multiple population reference genomes
  ☆34Updated last year
• PacificBiosciences / portello
  Transfer HiFi read mappings from their own assembly contigs to a standard reference
  ☆29Updated last month
• luntergroup / polyploid
  Benchmarking variant calling in polyploids
  ☆15Updated 4 years ago
• karel-brinda / samsift
  SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions.
  ☆23Updated 4 months ago
• oscarlr / MsPAC
  Phase reads, assemble haplotypes and detect SVs
  ☆19Updated 5 years ago
• CMU-SAFARI / FastRemap
  FastRemap, a C++ tool for quickly remapping reads between genome assemblies based on the commonly used CrossMap tool. Link to paper: http…
  ☆26Updated 3 years ago
• rlorigro / nanopore_assembly_and_polishing_assessment
  Automation of pipelines that depend on preexisting assembly, polishing, and alignment tools. Performance evaluation and visualization of …
  ☆13Updated 5 years ago
• gjun / muCNV
  ☆20Updated 2 years ago