Alternatives and similar repositories for GATK4_Best_Practice

Users that are interested in GATK4_Best_Practice are comparing it to the libraries listed below

• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆67Updated 8 months ago
• giesselmann / nanopype
  Snakemake pipelines for nanopore sequencing data archiving and processing
  ☆91Updated 3 years ago
• gencorefacility / variant-calling-pipeline-gatk4
  Variant Calling Pipeline Using GATK4 and Nextflow
  ☆58Updated 2 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆75Updated last year
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆51Updated 5 years ago
• wdecoster / nano-snakemake
  A snakemake pipeline for SV analysis from nanopore genome sequencing
  ☆52Updated 5 years ago
• SciLifeLab / TIDDIT
  TIDDIT - structural variant calling
  ☆78Updated last month
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 3 years ago
• nf-core / rnavar
  gatk4 RNA variant calling pipeline
  ☆59Updated last week
• lpryszcz / bin
  My bioinfo toolbox
  ☆50Updated 11 months ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆57Updated this week
• pinellolab / AmpUMI
  Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
  ☆42Updated 5 months 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
  ☆57Updated 6 years ago
• Genotek / ClassifyCNV
  ClassifyCNV: a tool for clinical annotation of copy-number variants
  ☆70Updated 2 years ago
• vplagnol / ExomeDepth
  ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
  ☆77Updated 7 months ago
• BimberLab / DISCVRSeq
  A collection of command line tools for working with sequencing data
  ☆52Updated last month
• mritchielab / long_read_tools
  A catalogue of available long read sequencing data analysis tools
  ☆85Updated 3 weeks ago
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆55Updated 7 months ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆143Updated 5 months ago
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆57Updated last year
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 7 years ago
• nf-core / hlatyping
  Precision HLA typing from next-generation sequencing data
  ☆77Updated 3 weeks ago
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆103Updated 5 years ago
• biocorecrg / master_of_pores
  Nextflow pipeline for analysis of direct RNA Nanopore reads
  ☆109Updated 2 months ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆93Updated 6 months ago
• Kingsford-Group / scallop
  Scallop is a reference-based transcriptome assembler for RNA-seq
  ☆92Updated 4 years ago
• nf-core / isoseq
  Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed …
  ☆49Updated 2 months ago
• nf-core / variantbenchmarking
  Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
  ☆38Updated last week
• Oshlack / Lace
  Building SuperTranscripts: A linear representation of transcriptome data
  ☆68Updated 4 years ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago