Alternatives and similar repositories for raredisease

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

• nf-core / smrnaseq
  A small-RNA sequencing analysis pipeline
  ☆98Updated this week
• nf-core / differentialabundance
  Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
  ☆87Updated last month
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆137Updated 3 years ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆175Updated last year
• nf-core / oncoanalyser
  A comprehensive cancer DNA/RNA analysis and reporting pipeline
  ☆97Updated this week
• gencorefacility / variant-calling-pipeline-gatk4
  Variant Calling Pipeline Using GATK4 and Nextflow
  ☆58Updated 2 years ago
• broadinstitute / long-read-pipelines
  Long read production pipelines
  ☆151Updated this week
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆200Updated this week
• Ensembl / VEP_plugins
  Plugins for the Ensembl Variant Effect Predictor (VEP)
  ☆163Updated 3 weeks ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆143Updated 2 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆137Updated last year
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆148Updated 4 months ago
• gagneurlab / drop
  Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
  ☆159Updated 2 weeks ago
• imgag / ClinCNV
  Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
  ☆91Updated 3 months ago
• epi2me-labs / wf-transcriptomes
  ☆109Updated last month
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆147Updated 4 months ago
• nf-core / test-datasets
  Test data to be used for automated testing with the nf-core pipelines
  ☆150Updated last week
• nf-core / fetchngs
  Pipeline to fetch metadata and raw FastQ files from public databases
  ☆184Updated last month
• ewels / AWS-iGenomes
  Documentation and description of AWS iGenomes S3 resource.
  ☆119Updated last year
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆109Updated last month
• friend1ws / nanomonsv
  SV detection tool for nanopore sequence reads
  ☆97Updated this week
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆157Updated 5 months ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆112Updated last year
• sbslee / pypgx
  A Python package for pharmacogenomics (PGx) research
  ☆82Updated last week
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated last year
• StevenWingett / FastQ-Screen
  Detecting contamination in NGS data and multi-species analysis
  ☆81Updated 2 months ago
• linsalrob / fastq-pair
  Match up paired end fastq files quickly and efficiently.
  ☆153Updated last year
• nf-core / bamtofastq
  Converts bam or cram files to fastq format and does quality control.
  ☆31Updated last month
• davetang / learning_vcf_file
  Learning the Variant Call Format
  ☆147Updated 5 months ago