Alternatives and similar repositories for GATK4_Best_Practice

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

• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆72Updated last year
• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆67Updated 4 months ago
• wdecoster / nano-snakemake
  A snakemake pipeline for SV analysis from nanopore genome sequencing
  ☆51Updated 5 years ago
• nf-core / hlatyping
  Precision HLA typing from next-generation sequencing data
  ☆71Updated last month
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 2 years ago
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated 11 months ago
• zd1 / telseq
  A software for calculating telomere length
  ☆71Updated 6 years ago
• BimberLab / DISCVRSeq
  A collection of command line tools for working with sequencing data
  ☆51Updated last month
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 7 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
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆51Updated 5 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.
  ☆73Updated 2 months ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago
• smithlabcode / dnmtools
  Tools for analyzing DNA methylation data
  ☆43Updated this week
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆50Updated 2 years ago
• lpryszcz / bin
  My bioinfo toolbox
  ☆50Updated 7 months ago
• biocorecrg / master_of_pores
  Nextflow pipeline for analysis of direct RNA Nanopore reads
  ☆106Updated 2 months ago
• Genotek / ClassifyCNV
  ClassifyCNV: a tool for clinical annotation of copy-number variants
  ☆66Updated 2 years ago
• TheJacksonLaboratory / SVE
  ☆51Updated 6 years ago
• gatk-workflows / broad-prod-wgs-germline-snps-indels
  Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…
  ☆56Updated 5 years ago
• nspies / svviz2
  for visual evaluation of read support for structural variation
  ☆54Updated last year
• nanoporetech / pinfish
  Tools to annotate genomes using long read transcriptomics data
  ☆46Updated 4 years ago
• tanghaibao / bio-pipeline
  My collection of light bioinformatics analysis pipelines for specific tasks
  ☆75Updated last year
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 6 years ago
• Illumina / ExpansionHunterDenovo
  A suite of tools for detecting expansions of short tandem repeats
  ☆82Updated 2 years ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆50Updated this week
• juliangehring / GMAP-GSNAP
  *UNOFFICIAL, UNMAINTAINED and OUTDATED*: This was an unofficial archive of GMAP-GSNAP releases. Please use the original website for curr…
  ☆33Updated 9 years ago
• gatk-workflows / gatk4-exome-analysis-pipeline
  This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…
  ☆55Updated 4 years ago
• nanoporetech / pipeline-pinfish-analysis
  Pipeline for annotating genomes using long read transcriptomics data with pinfish
  ☆28Updated 4 years ago