Alternatives and similar repositories for variant-calling-pipeline-gatk4

Users that are interested in variant-calling-pipeline-gatk4 are comparing it to the libraries listed below

• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆67Updated 3 weeks ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆87Updated 8 months ago
• giesselmann / nanopype
  Snakemake pipelines for nanopore sequencing data archiving and processing
  ☆90Updated 3 years ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆85Updated 6 years ago
• moiexpositoalonsolab / grenepipe
  A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - fo…
  ☆99Updated 3 weeks ago
• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆97Updated last year
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆69Updated 9 months ago
• sujaikumar / assemblage
  Tools for working with second gen assemblies, fasta sequences, etc
  ☆93Updated 8 years ago
• biocorecrg / master_of_pores
  Nextflow pipeline for analysis of direct RNA Nanopore reads
  ☆102Updated last month
• ISUgenomics / common_analyses
  Repository of common bioinformatics scripts
  ☆39Updated 3 years ago
• Trinotate / Trinotate.github.io
  web documentation for Trinotate
  ☆48Updated 2 years ago
• epi2me-labs / wf-basecalling
  ☆39Updated 3 weeks ago
• EI-CoreBioinformatics / mikado
  Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to s…
  ☆101Updated 3 months ago
• compbiocore / VariantVisualization.jl
  Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:
  ☆86Updated last year
• nf-core / smrnaseq
  A small-RNA sequencing analysis pipeline
  ☆85Updated this week
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 6 years ago
• parklab / xTea
  Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
  ☆111Updated last month
• mhammell-laboratory / TElocal
  A package for quantifying transposable elements at a locus level for RNAseq datasets.
  ☆26Updated 4 months ago
• Oshlack / Corset
  Software for clustering de novo assembled transcripts and counting overlapping reads
  ☆71Updated 3 years ago
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆51Updated 4 years ago
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆117Updated last month
• Dfam-consortium / TETools
  Dfam Transposable Element Tools Docker container.
  ☆91Updated last month
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆56Updated 2 years ago
• JimWhiting91 / genotype_plot
  A set of functions to visualise genotypes based on a VCF
  ☆86Updated 3 years ago
• lfaino / LoReAn
  Long Reads Annotation pipeline
  ☆72Updated 3 years ago
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆99Updated this week
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 7 months ago
• MikeAxtell / ShortStack
  ShortStack: Comprehensive annotation and quantification of small RNA genes
  ☆92Updated last week
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆150Updated 3 months ago
• epi2me-labs / modbam2bed
  ☆48Updated 9 months ago