Alternatives and similar repositories for strelka

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

• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆320Updated last month
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆475Updated 2 weeks ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆319Updated 3 years ago
• Illumina / manta
  Structural variant and indel caller for mapped sequencing data
  ☆434Updated 2 years ago
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆242Updated last week
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• STAR-Fusion / STAR-Fusion
  STAR-Fusion codebase
  ☆243Updated 2 weeks ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆389Updated 7 months ago
• pcingola / SnpEff
  ☆279Updated 5 months ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆437Updated last year
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆254Updated 2 years ago
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆224Updated 3 years ago
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆244Updated 8 months ago
• genome-in-a-bottle / giab_data_indexes
  This repository contains data indexes from NIST's Genome in a Bottle project.
  ☆250Updated last year
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆269Updated last month
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆244Updated 3 months ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆160Updated 2 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆544Updated last year
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆202Updated 4 years ago
• WGLab / InterVar
  A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
  ☆196Updated 2 years ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆230Updated last week
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆313Updated 4 months ago
• gatk-workflows / gatk4-data-processing
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  ☆153Updated 2 years ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆444Updated last year
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆425Updated last month
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆425Updated 2 months ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆242Updated 2 years ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆343Updated 2 months ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆412Updated last year
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆317Updated 2 years ago