Alternatives and similar repositories for encoded:

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

• CCDG / Pipeline-Standardization
  ☆82Updated 6 years ago
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆97Updated 11 months ago
• TrinityCTAT / Trinity_CTAT
  ☆116Updated last year
• CGATOxford / cgat
  Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps
  ☆124Updated 6 years ago
• broadinstitute / mutect
  MuTect -- Accurate and sensitive cancer mutation detection
  ☆96Updated 2 years ago
• Ensembl / ensembl-pipeline
  *DEPRECATED* Job management for the Ensembl Genebuild pipeline
  ☆62Updated last year
• konradjk / exac_browser
  Browser for ExAC consortium data
  ☆106Updated 3 years ago
• slowkow / snakefiles
  Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).
  ☆92Updated 7 years ago
• nunofonseca / irap
  integrated RNA-seq Analysis Pipeline
  ☆84Updated 6 years ago
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆135Updated 3 years ago
• broadinstitute / gnomad_methods
  Hail helper functions for the gnomAD project and Translational Genomics Group
  ☆94Updated 2 weeks ago
• gogetdata / ggd-recipes
  conda recipes for genomic data
  ☆85Updated 3 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆145Updated 2 years ago
• AstraZeneca-NGS / VarDictJava
  VarDict Java port
  ☆134Updated last year
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆151Updated 2 years ago
• dnanexus-rnd / GLnexus
  Scalable gVCF merging and joint variant calling for population sequencing projects
  ☆157Updated last year
• Illumina / Cyrius
  A tool to genotype CYP2D6 with WGS data
  ☆51Updated last year
• zwdzwd / transvar
  TransVar - multiway annotator for precision medicine
  ☆125Updated 2 years ago
• dnanexus / dx-toolkit
  DNAnexus platform client libraries
  ☆93Updated this week
• Clinical-Genomics / genmod
  Annotate models of genetic inheritance patterns in variant files (vcf files)
  ☆79Updated last week
• GenomiqueENS / eoulsan
  A pipeline and a framework for NGS analysis (RNA-seq and scRNA-seq)
  ☆52Updated last month
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆70Updated 4 years ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆203Updated 4 years ago
• broadinstitute / gnomad_qc
  ☆69Updated this week
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆196Updated last week
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆159Updated 8 months ago
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆38Updated 3 years ago
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆122Updated 3 years ago
• maximilianh / cellBrowser
  main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datase…
  ☆111Updated 2 years ago
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 2 years ago