Alternatives and similar repositories for strelka

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

• Illumina / manta
  Structural variant and indel caller for mapped sequencing data
  ☆436Updated 2 years ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆478Updated last week
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆319Updated 3 years ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆320Updated 2 months ago
• STAR-Fusion / STAR-Fusion
  STAR-Fusion codebase
  ☆244Updated last month
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆243Updated last week
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆256Updated 2 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆544Updated last year
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆415Updated last year
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆270Updated 2 months ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆438Updated last year
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆314Updated last week
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆392Updated last week
• pcingola / SnpEff
  ☆284Updated 6 months ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆245Updated 2 weeks ago
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆225Updated 3 years ago
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆244Updated 9 months ago
• WGLab / InterVar
  A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
  ☆197Updated 2 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆161Updated 2 years ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆448Updated last year
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆427Updated 2 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆271Updated last year
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆299Updated 2 years ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆278Updated last year
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆243Updated 2 years ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆233Updated this week
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆197Updated last week
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆271Updated 6 months ago
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆333Updated 3 years ago