Alternatives and similar repositories for megSAP

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

• imgag / ClinCNV
  Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
  ☆85Updated 3 months ago
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆38Updated 3 years ago
• Illumina / ExpansionHunterDenovo
  A suite of tools for detecting expansions of short tandem repeats
  ☆80Updated last year
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆114Updated 3 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆69Updated 8 months ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆187Updated this week
• SBIMB / StellarPGx
  Calling star alleles in highly polymorphic pharmacogenes (e.g. CYP450 genes) by leveraging genome graph-based variant detection.
  ☆33Updated last month
• biocorecrg / master_of_pores
  Nextflow pipeline for analysis of direct RNA Nanopore reads
  ☆102Updated last week
• gencorefacility / variant-calling-pipeline-gatk4
  Variant Calling Pipeline Using GATK4 and Nextflow
  ☆54Updated 2 years ago
• compbiocore / VariantVisualization.jl
  Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:
  ☆86Updated last year
• Ensembl / VEP_plugins
  Plugins for the Ensembl Variant Effect Predictor (VEP)
  ☆147Updated last week
• Sentieon / sentieon-scripts
  Helper scripts for biological data processing from Sentieon
  ☆64Updated 6 months ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆114Updated 9 months ago
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆213Updated 4 months ago
• genome-in-a-bottle / genome-stratifications
  Stratification BED files from the Global Alliance for Genomics and Health (GA4GH) Benchmarking Team and the Genome in a Bottle Consortium…
  ☆79Updated 2 years ago
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆97Updated 7 months ago
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆97Updated 11 months ago
• Clinical-Genomics / MIP
  Mutation Identification Pipeline. Read the latest documentation:
  ☆44Updated last year
• human-pangenomics / hpgp-data
  Data from the Human PanGenomics Project
  ☆60Updated 3 years ago
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆128Updated 3 months ago
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆81Updated 2 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
• sbslee / pypgx
  A Python package for pharmacogenomics (PGx) research
  ☆73Updated 2 months ago
• nf-core / smrnaseq
  A small-RNA sequencing analysis pipeline
  ☆84Updated last week
• SciLifeLab / TIDDIT
  TIDDIT - structural variant calling
  ☆73Updated last month
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 2 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆159Updated 8 months ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 6 months ago
• aryeelab / guideseq
  Analysis pipeline for the GUIDE-seq assay.
  ☆78Updated last year
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago