Alternatives and similar repositories for reference_data:

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

• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆97Updated 2 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 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…
  ☆52Updated 4 years ago
• FoundationMedicineInc / SGZ
  ☆40Updated last year
• dariober / cnv_facets
  Somatic copy variant caller (CNV) for next generation sequencing
  ☆70Updated 6 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  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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…
  ☆77Updated 5 years ago
• sztup / scarHRD
  ☆112Updated last year
• dinhdiep / MONOD2
  MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data
  ☆38Updated 6 years ago
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆96Updated 6 months ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆70Updated 4 years ago
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆56Updated 3 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆129Updated 9 months ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 5 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 4 months ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆140Updated 2 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆49Updated 7 months ago
• broadinstitute / PhylogicNDT
  ☆71Updated 10 months ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆67Updated 6 months ago
• bioinfo-pf-curie / TMB
  Tumor Mutational Burden
  ☆58Updated 6 months ago
• broadinstitute / gistic2
  Genomic Identification of Significant Targets in Cancer (GISTIC), version 2
  ☆50Updated 2 years ago
• parklab / ShatterSeek
  ☆67Updated last year
• MonashBioinformaticsPlatform / RSeQC
  fork of RSeQC python RNAseq metrics suit of tools
  ☆48Updated 6 years ago
• OpenGene / ctdna-pipeline
  A simplified pipeline for ctDNA sequencing data analysis
  ☆36Updated 7 years ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆54Updated 2 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 4 months ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆41Updated 9 years ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆61Updated 2 years ago
• Kennedy-Lab-UW / Duplex-Sequencing
  ☆57Updated 4 years ago
• RahmanTeam / DECoN
  ☆53Updated 2 years ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆101Updated 11 months ago