Alternatives and similar repositories for gatk-protected

Users that are interested in gatk-protected are comparing it to the libraries listed below

• DaehwanKimLab / hisat
  Fast spliced aligner with low memory requirements
  ☆41Updated 9 years ago
• gatk-workflows / five-dollar-genome-analysis-pipeline
  Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline
  ☆56Updated 5 years ago
• mozack / abra
  Assembly Based ReAligner
  ☆74Updated 7 years ago
• ngsutils / ngsutils
  Tools for next-generation sequencing analysis
  ☆88Updated 6 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• sequencing / isaac_variant_caller
  This project is deprecated, please see strelka2 at https://github.com/Illumina/strelka
  ☆37Updated 8 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆108Updated 4 years ago
• Cibiv / Teaser
  A tool to benchmark mappers and different parameters within minutes
  ☆44Updated 5 years ago
• 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
• 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
• gt1 / biobambam2
  Tools for early stage alignment file processing
  ☆95Updated 6 years ago
• ckandoth / variant-filter
  A false-positive filter for variants called from massively parallel sequencing
  ☆29Updated 8 years ago
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆53Updated 6 years ago
• brwnj / umitools
  Tools to handle reads sequenced with unique molecular identifiers (UMIs).
  ☆30Updated 8 years ago
• CGATOxford / cgat
  Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps
  ☆124Updated 6 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 years ago
• kingsfordgroup / sailfish
  Rapid Mapping-based Isoform Quantification from RNA-Seq Reads
  ☆126Updated 3 years ago
• h3abionet / h3agatk
  ☆21Updated 4 years ago
• svviz / svviz
  Read visualizer for structural variants
  ☆84Updated 6 years ago
• Illumina / isaac2
  Aligner for sequencing data
  ☆21Updated 9 years ago
• statgen / gotcloud
  Genomes on the Cloud, Mapping & Variant Calling Pipelines
  ☆34Updated 8 years ago
• schatzlab / appliedgenomics2017
  JHU EN.600.649: Computational Genomics: Applied Comparative Genomics
  ☆57Updated 7 years ago
• KHP-Informatics / ngseasy
  Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
  ☆87Updated 7 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• BD2KGenomics / toil-scripts
  Toil workflows for common genomic pipelines
  ☆33Updated 5 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆72Updated 3 years ago
• sfu-compbio / sinvict
  SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA
  ☆27Updated 4 years ago
• broadinstitute / oncotator
  ☆68Updated 3 years ago
• slzhao / QC3
  QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
  ☆32Updated 9 years ago