Alternatives and similar repositories for delly

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

• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆381Updated 3 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆317Updated 3 years ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆459Updated 3 weeks ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆545Updated last year
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆325Updated 3 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆259Updated 2 years ago
• Illumina / manta
  Structural variant and indel caller for mapped sequencing data
  ☆440Updated 2 years ago
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆378Updated 2 weeks ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆442Updated last year
• TransDecoder / TransDecoder
  TransDecoder source
  ☆297Updated 3 weeks ago
• pcingola / SnpEff
  ☆290Updated 2 weeks ago
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆429Updated 4 months ago
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆317Updated 2 years ago
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆333Updated 3 years ago
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆615Updated 3 weeks ago
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆504Updated 2 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆275Updated last year
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆396Updated last year
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆383Updated 3 weeks ago
• WGLab / InterVar
  A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
  ☆197Updated 2 years ago
• usadellab / Trimmomatic
  ☆266Updated last month
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆433Updated last month
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆272Updated 3 months ago
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆227Updated 3 years ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆434Updated 8 months ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆398Updated last month
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆244Updated last month
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆262Updated last week
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆376Updated 3 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆276Updated 7 months ago