Alternatives and similar repositories for octopus

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

• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆329Updated 6 months ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆165Updated 2 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆320Updated 3 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆249Updated 2 months ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆272Updated 2 months ago
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆230Updated 3 years ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆280Updated 6 months ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆208Updated 4 years ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆260Updated last year
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆148Updated 10 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆201Updated last year
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆354Updated 7 months ago
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆403Updated 2 years ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆284Updated 10 months ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆196Updated last week
• vibansal / HapCUT2
  software tools for haplotype assembly from sequence data
  ☆224Updated 10 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆557Updated last year
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆261Updated 2 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆251Updated 4 months ago
• genome-in-a-bottle / giab_data_indexes
  This repository contains data indexes from NIST's Genome in a Bottle project.
  ☆259Updated 2 years ago
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆391Updated this week
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆253Updated 2 months ago
• Illumina / ExpansionHunter
  A tool for estimating repeat sizes
  ☆199Updated last year
• lh3 / wgsim
  Reads simulator
  ☆282Updated 4 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆276Updated 2 years ago
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆139Updated 4 years 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…
  ☆306Updated last year
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆137Updated 2 years ago
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆201Updated 4 months ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆391Updated 3 months ago