Alternatives and similar repositories for graphite

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

• brwnj / covviz
  Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
  ☆58Updated 3 years ago
• lh3 / sgdp-fermi
  FermiKit small variant calls for public SGDP samples
  ☆17Updated 8 years ago
• zeeev / mergeSVcallers
  heuristics to merge structural variant calls in VCF format.
  ☆36Updated 8 years ago
• lh3 / rtgeval
  Wrapper for RTG's vcfeval; DEPRECATED!
  ☆21Updated 9 years ago
• lganel / SVScore
  Prioritize structural variants based on CADD scores
  ☆29Updated 5 years ago
• lh3 / htsbox
  My experimental tools on top of htslib. NOT OFFICIAL!!!
  ☆56Updated 2 years ago
• DecodeGenetics / popSTR
  PopSTR - A Population based microsatellite genotyper
  ☆33Updated last year
• vibansal / hapcut
  program for haplotype phasing from sequence reads and related tools
  ☆25Updated 6 years ago
• kehrlab / PopDel
  Population-wide Deletion Calling
  ☆35Updated 4 months ago
• grocsvs / grocsvs
  Genome-wide reconstruction of complex structural variants
  ☆39Updated 3 years ago
• aquaskyline / 16GT
  Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
  ☆27Updated last year
• Illumina / witty.er
  What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
  ☆32Updated last year
• benedictpaten / marginPhase
  ☆34Updated 5 years ago
• ljdursi / mergevcf
  Python package and routines for merging VCF files
  ☆29Updated 4 years ago
• PacificBiosciences / svpack
  Structural variant (SV) analysis tools
  ☆36Updated last year
• HongzheGuo / deBGA
  de Bruijn Graph-based read aligner
  ☆33Updated 6 years ago
• quinlan-lab / vcf2db
  create a gemini-compatible database from a VCF
  ☆56Updated 4 years ago
• bkehr / popins
  Population-scale detection of novel sequence insertions
  ☆27Updated 3 years ago
• lh3 / etrf
  Exact Tandem Repeat Finder (not a TRF replacement)
  ☆49Updated 5 years ago
• jkbonfield / crumble
  Exploration of controlled loss of quality values for compressing CRAM files
  ☆35Updated 2 years ago
• ccgd-profile / BreaKmer
  A method to identify structural variation from sequencing data in target regions
  ☆32Updated 4 years ago
• jbelyeu / SV-plaudit
  Pipeline for structural variant image curation and analysis.
  ☆48Updated 3 years ago
• xuchang116 / smCounter
  smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very…
  ☆20Updated 6 years ago
• jhhung / PEAT
  An ultra fast and accurate paired-end adapter trimmer that needs no a priori adapter sequences.
  ☆22Updated 4 years ago
• vgteam / gssw
  efficient alignment of strings to partially ordered string graphs
  ☆33Updated 3 years ago
• VCCRI / SVPV
  Structural Variant Prediction Viewer
  ☆35Updated 8 years ago
• talkowski-lab / svtk
  ☆35Updated 4 years ago
• cdarby / samovar
  Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters
  ☆24Updated 6 years ago
• GregoryFaust / SVsim
  SVsim: a tool that generates synthetic Structural Variant calls as benchmarks to test/evaluate SV calling pipelines.
  ☆17Updated 7 years ago
• 10XGenomics / lariat
  Linked-Read Alignment Tool
  ☆27Updated 6 years ago