Alternatives and similar repositories for genipe

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

• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆49Updated 6 years ago
• sigven / gvanno
  Generic human DNA variant annotation pipeline
  ☆58Updated last year
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆52Updated 4 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated last year
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆72Updated 3 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 2 years ago
• statgen / gotcloud
  Genomes on the Cloud, Mapping & Variant Calling Pipelines
  ☆34Updated 8 years ago
• ding-lab / MuSiC2
  identifying mutational significance in cancer genomes
  ☆61Updated 2 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆71Updated 4 years ago
• Ettwiller / Damage-estimator
  Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…
  ☆53Updated 8 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• nellore / intropolis
  Exon-exon splice junctions across SRA
  ☆40Updated 3 years ago
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆56Updated 4 years ago
• genome / somatic-sniper
  A tool to call somatic single nucleotide variants.
  ☆41Updated 9 years ago
• cancerit / alleleCount
  Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…
  ☆45Updated 2 years ago
• parklab / ShatterSeek
  ☆69Updated last year
• ckandoth / variant-filter
  A false-positive filter for variants called from massively parallel sequencing
  ☆29Updated 8 years ago
• SciLifeLab / NGI-RNAseq
  Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
  ☆51Updated 6 years ago
• svviz / svviz
  Read visualizer for structural variants
  ☆84Updated 6 years ago
• CshlSiepelLab / LINSIGHT
  ☆25Updated this week
• 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…
  ☆53Updated 4 years ago
• Clinical-Genomics / genmod
  Annotate models of genetic inheritance patterns in variant files (vcf files)
  ☆79Updated last month
• YangLab / CIRCexplorer
  A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, …
  ☆61Updated 6 years ago
• CGATOxford / CGATPipelines
  Collection of CGAT NGS Pipelines
  ☆43Updated 6 years ago
• griffithlab / pVAC-Seq
  DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools
  ☆61Updated 6 years ago
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆53Updated 6 years ago
• PubuduSaneth / cnvScan
  CNV screening and annotation tool
  ☆25Updated 8 years ago