Alternatives and similar repositories for manta

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

• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆368Updated 3 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆540Updated 10 months ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆316Updated 11 months ago
• pcingola / SnpEff
  ☆272Updated 3 months ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆463Updated 2 weeks ago
• WGLab / InterVar
  A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
  ☆193Updated last year
• AstraZeneca-NGS / VarDict
  VarDict
  ☆199Updated last year
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆252Updated 2 months ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆268Updated last year
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆386Updated 5 months ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆274Updated 10 months ago
• STAR-Fusion / STAR-Fusion
  STAR-Fusion codebase
  ☆240Updated last week
• gatk-workflows / gatk4-data-processing
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  ☆150Updated 2 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆265Updated last year
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆419Updated 3 weeks ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆428Updated last year
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆253Updated last year
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆238Updated last month
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆199Updated last year
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆440Updated last year
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆244Updated last month
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆221Updated 3 years ago
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆316Updated 2 years ago
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆325Updated 2 years ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆241Updated 2 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆315Updated 3 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆158Updated 2 years ago
• usadellab / Trimmomatic
  ☆243Updated 11 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆227Updated 4 years ago
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆363Updated 4 months ago