Alternatives and similar repositories for SnpEff:

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

• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆250Updated last year
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆267Updated last year
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆235Updated last week
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆314Updated 3 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆156Updated last year
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆221Updated 4 years ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆267Updated last month
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆183Updated this week
• AstraZeneca-NGS / VarDict
  VarDict
  ☆194Updated last year
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆310Updated 9 months ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆246Updated 2 weeks ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆540Updated 8 months ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆131Updated 10 years ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆460Updated 3 weeks ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆264Updated last year
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆209Updated 4 years ago
• gatk-workflows / gatk4-data-processing
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  ☆150Updated 2 years ago
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆316Updated 2 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆212Updated 8 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆208Updated 3 weeks ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆201Updated 4 years ago
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆197Updated this week
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆257Updated 2 months ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆354Updated 2 years ago
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆346Updated 2 weeks ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆371Updated last year
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆194Updated last month
• usadellab / Trimmomatic
  ☆238Updated 9 months ago
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆239Updated 5 months ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆221Updated last week