Alternatives and similar repositories for Duplex-Sequencing

Users that are interested in Duplex-Sequencing are comparing it to the libraries listed below

• FoundationMedicineInc / SGZ
  ☆43Updated last year
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆99Updated 3 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆88Updated 8 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆148Updated 4 months ago
• gatk-workflows / gatk4-somatic-snvs-indels
  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…
  ☆78Updated 5 years ago
• griffithlab / pVAC-Seq
  DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools
  ☆61Updated 6 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 10 years ago
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆57Updated 4 years ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆62Updated 3 years ago
• broadinstitute / oncotator
  ☆69Updated 3 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆117Updated last year
• shendurelab / cfDNA
  Analysis of epigenetic signals captured by fragmentation patterns of cell-free DNA
  ☆77Updated 5 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated last year
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆143Updated 2 years ago
• griffithlab / regtools
  Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
  ☆135Updated last year
• ding-lab / CharGer
  Characterization of Germline variants
  ☆99Updated 3 years ago
• gatk-workflows / gatk4-exome-analysis-pipeline
  This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…
  ☆55Updated 5 years ago
• imgag / ClinCNV
  Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
  ☆91Updated 3 months ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆100Updated 4 years ago
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆131Updated 3 years ago
• bgruening / galaxy-rna-workbench
  Galaxy RNA workbench
  ☆41Updated 5 years ago
• xjtu-omics / msisensor-pro
  Microsatellite Instability (MSI) detection using high-throughput sequencing data.
  ☆115Updated 9 months ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆137Updated last year
• ding-lab / msisensor
  microsatellite instability detection using tumor only or paired tumor-normal data
  ☆132Updated 5 years ago
• OpenGene / ctdna-pipeline
  A simplified pipeline for ctDNA sequencing data analysis
  ☆37Updated 8 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 5 years ago
• pughlab / ConsensusCruncher
  ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…
  ☆21Updated 3 years ago
• dieterich-lab / DCC
  DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies …
  ☆37Updated 3 years ago
• OSU-SRLab / MANTIS
  Microsatellite Analysis for Normal-Tumor InStability
  ☆75Updated 3 years ago