Alternatives and similar repositories for octopus

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

• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆378Updated last year
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆541Updated 10 months ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆158Updated 2 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆217Updated last week
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆268Updated last year
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆250Updated 11 months ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆252Updated 2 months ago
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆356Updated last week
• AstraZeneca-NGS / VarDict
  VarDict
  ☆199Updated last year
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆317Updated 11 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆270Updated 3 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆212Updated last month
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆265Updated last year
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆245Updated 2 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆253Updated last year
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆193Updated 2 months ago
• philres / ngmlr
  NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…
  ☆301Updated last year
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆326Updated 2 years ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆203Updated 4 years ago
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆221Updated 3 years ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆252Updated last week
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆332Updated 2 weeks ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆362Updated 3 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆315Updated 3 years ago
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆278Updated 6 months ago
• vibansal / HapCUT2
  software tools for haplotype assembly from sequence data
  ☆218Updated 3 months ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆249Updated last year
• whatshap / whatshap
  Read-based phasing of genomic variants, also called haplotype assembly
  ☆364Updated last week
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆209Updated 5 years ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆227Updated 4 years ago