Alternatives and similar repositories for GATK-flow

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

• MarioniLab / sarlacc
  The R package "sarlacc" contains a pipeline to analyse nanopore sequencing data. It trims adapter sequences, retrieves optional UMI's, cl…
  ☆15Updated 6 years ago
• ccbiolab / svpluscnv
  Integrative analysis of complex structural variants
  ☆22Updated 5 years ago
• smithlabcode / abismal
  Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.
  ☆19Updated last week
• NCGG-MGC / IMSindel
  IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split …
  ☆16Updated 2 years ago
• AlgoLab / shark
  Mapping-free software for fishing relevant reads in an RNA-Seq sample
  ☆19Updated 5 years ago
• dermasugita / Viola-SV
  Viola is a flexible and powerful python package designed specifically for analysis of genomic structural variant (SV) signatures.
  ☆26Updated last year
• J35P312 / FindSV
  Structural variant pipeline
  ☆17Updated 5 years ago
• viq854 / lichee
  Multi-sample cancer phylogeny reconstruction
  ☆36Updated 8 years ago
• NCBI-Hackathons / HLAClustRView
  R package specialized in HLA typing clustering and visualization based on specific similarity metrics
  ☆14Updated 6 years ago
• griffithlab / VAtools
  A set of tools to annotate VCF files with expression and readcount data
  ☆29Updated 9 months ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 3 years ago
• dantaki / CNVplot
  Plot CNV data with a genome viewer in R
  ☆15Updated 8 years ago
• bartongroup / 2passtools
  Two pass alignment for long reads
  ☆22Updated 4 years ago
• Gregor-Mendel-Institute / bookend
  End-guided RNA assembler
  ☆15Updated last week
• Oshlack / MINTIE
  Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.
  ☆36Updated last year
• YingZhou001 / Immuannot
  Immuological gene typing and annotation for genome assembly
  ☆38Updated 8 months ago
• WGLab / LongGF
  A computational algorithm and software tool for fast and accurate detection of gene fusion by long-read transcriptome sequencing
  ☆21Updated 4 years ago
• robsyme / nf-repeatmasking
  Nextflow workflow for automatic repeat detection, classification and masking
  ☆13Updated 7 years ago
• KolmogorovLab / minda
  ☆25Updated 7 months ago
• IARCbioinfo / alignment-nf
  Whole Exome/Whole Genome Sequencing alignment pipeline
  ☆28Updated last year
• nygenome / Lancet2
  v2.x of the microassembly based somatic variant caller
  ☆23Updated 4 months ago
• VanLoo-lab / CAMDAC
  ☆11Updated 2 months ago
• vpc-ccg / svict
  Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA
  ☆29Updated last year
• FischerJo / FAME
  ☆14Updated 2 years ago
• IrinaVKuznetsova / CirGO
  ☆21Updated last year
• mikessh / mageri
  MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers
  ☆21Updated 8 years ago
• rdemolgen / SavvySuite
  Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes
  ☆31Updated 3 months ago
• cortes-ciriano-lab / ReConPlot
  ☆24Updated 11 months ago
• aakechin / cutPrimers
  curPrimers is a tool for trimming primer sequences from amplicon based NGS reads
  ☆17Updated 6 months ago
• UMCUGenetics / COLO829_somaticSV
  Scripts and files used in the generation of the COLO829 somatic SV truthset.
  ☆13Updated 3 years ago