Alternatives and similar repositories for GATK4_Best_Practice

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

• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 7 months ago
• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆67Updated 5 months ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆72Updated last year
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated 11 months ago
• nf-core / hlatyping
  Precision HLA typing from next-generation sequencing data
  ☆72Updated 2 months ago
• wdecoster / nano-snakemake
  A snakemake pipeline for SV analysis from nanopore genome sequencing
  ☆51Updated 5 years ago
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆54Updated 4 months ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago
• lpryszcz / bin
  My bioinfo toolbox
  ☆50Updated 8 months ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆53Updated last week
• SciLifeLab / TIDDIT
  TIDDIT - structural variant calling
  ☆76Updated 6 months ago
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆51Updated 5 years ago
• pwwang / vcfstats
  Powerful statistics for VCF files
  ☆70Updated 3 months ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 3 years ago
• gencorefacility / variant-calling-pipeline-gatk4
  Variant Calling Pipeline Using GATK4 and Nextflow
  ☆58Updated 2 years ago
• BimberLab / DISCVRSeq
  A collection of command line tools for working with sequencing data
  ☆52Updated last week
• nspies / svviz2
  for visual evaluation of read support for structural variation
  ☆55Updated last year
• nf-core / oncoanalyser
  A comprehensive cancer DNA/RNA analysis and reporting pipeline
  ☆87Updated this week
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆63Updated last year
• giesselmann / nanopype
  Snakemake pipelines for nanopore sequencing data archiving and processing
  ☆91Updated 3 years ago
• s-andrews / BamQC
  Mapped QC analysis program
  ☆44Updated 7 years ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆142Updated last month
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆73Updated 3 years ago
• Genotek / ClassifyCNV
  ClassifyCNV: a tool for clinical annotation of copy-number variants
  ☆67Updated 2 years ago
• smithlabcode / preseq
  Software for predicting library complexity and genome coverage in high-throughput sequencing.
  ☆88Updated 11 months ago
• Illumina / ExpansionHunterDenovo
  A suite of tools for detecting expansions of short tandem repeats
  ☆83Updated 2 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆52Updated last year
• cccnrc / plot-VCF
  visual analysis of your VCF files
  ☆36Updated 2 years ago
• dieterich-lab / JACUSA2
  New version of JACUSA -> 2.0
  ☆29Updated last week