Alternatives and similar repositories for GATK-flow

Users that are interested in GATK-flow are comparing it to the libraries listed below

• ccbiolab / svpluscnv
  Integrative analysis of complex structural variants
  ☆21Updated 4 years ago
• Transipedia / dekupl
  Exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.
  ☆15Updated 6 years ago
• clemgoub / TypeTE
  Genotyping of segregating mobile elements insertions
  ☆19Updated 3 years ago
• KolmogorovLab / minda
  ☆17Updated 3 weeks ago
• cortes-ciriano-lab / ReConPlot
  ☆22Updated 4 months ago
• nygenome / Lancet2
  v2.x of the microassembly based somatic variant caller
  ☆21Updated 2 weeks ago
• sanjaynagi / rna-seq-pop
  Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
  ☆18Updated last month
• czc / nb_distribution
  novoBreak: local assembly for breakpoint detection in cancer genomes
  ☆26Updated 7 years ago
• IARCbioinfo / alignment-nf
  Whole Exome/Whole Genome Sequencing alignment pipeline
  ☆28Updated 7 months ago
• Mesh89 / TranSurVeyor
  A transposition caller.
  ☆10Updated last year
• smithlabcode / abismal
  Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.
  ☆18Updated 2 months ago
• robsyme / nf-repeatmasking
  Nextflow workflow for automatic repeat detection, classification and masking
  ☆13Updated 7 years ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 3 years ago
• griffithlab / VAtools
  A set of tools to annotate VCF files with expression and readcount data
  ☆29Updated 2 months ago
• a2iEditing / deNovo-Detect
  ☆12Updated 2 years ago
• J35P312 / FindSV
  Structural variant pipeline
  ☆17Updated 4 years ago
• namphuon / ViFi
  Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.
  ☆27Updated 3 years ago
• rdemolgen / SavvySuite
  Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes
  ☆29Updated 10 months ago
• mritchielab / GlimmaV2
  interactive plots for differential expression analysis
  ☆32Updated last month
• dantaki / CNVplot
  Plot CNV data with a genome viewer in R
  ☆15Updated 8 years ago
• HurlesGroupSanger / indelible
  Structural Variation breakpoint discovery via adaptive learning
  ☆15Updated last year
• SexChrLab / XYalign
  ☆23Updated 5 years ago
• Genomon-Project / GenomonSV
  structure detection program
  ☆17Updated 5 months ago
• mgaleyuw / MeOW
  Automated Detection and Qualification of Differential Methylation
  ☆14Updated last year
• SdeBlank / NanoFG
  Third-generation fusion gene detection
  ☆14Updated last year
• bio-ontology-research-group / DeepSVP
  Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity
  ☆16Updated 3 years ago
• YingZhou001 / Immuannot
  Immuological gene typing and annotation for genome assembly
  ☆35Updated 2 months ago
• d3b-center / annoFuse
  Filter and prioritize fusion calls
  ☆20Updated 7 months ago
• scottgigante / haplotyped-methylome
  Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation
  ☆23Updated 6 years ago
• bartongroup / 2passtools
  Two pass alignment for long reads
  ☆22Updated 4 years ago