Alternatives and similar repositories for TS

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

• NCBI-Hackathons / EDirectCookbook
  ☆165Updated 5 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆247Updated last month
• GregoryFaust / samblaster
  samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
  ☆234Updated 4 years ago
• zstephens / neat-genreads
  NEAT read simulation tools
  ☆98Updated 3 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆200Updated 4 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
• jstjohn / SeqPrep
  Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
  ☆144Updated 8 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• genome-in-a-bottle / giab_data_indexes
  This repository contains data indexes from NIST's Genome in a Bottle project.
  ☆253Updated last year
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆314Updated last week
• Ensembl / VEP_plugins
  Plugins for the Ensembl Variant Effect Predictor (VEP)
  ☆155Updated this week
• PacificBiosciences / ccs
  CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
  ☆121Updated last year
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆262Updated 3 weeks ago
• genome / pindel
  Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …
  ☆173Updated 5 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆161Updated 2 years ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆154Updated 3 years ago
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆134Updated 2 years ago
• PacificBiosciences / DevNet
  The DevNet project on github stores the PacBio DevNet website.
  ☆116Updated 7 years ago
• andyrimmer / Platypus
  Platypus Variant Caller
  ☆108Updated last year
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 6 years ago
• Illumina / Nirvana
  The nimble & robust variant annotator
  ☆183Updated last year
• humanlongevity / HLA
  xHLA: Fast and accurate HLA typing from short read sequence data
  ☆113Updated last year
• nh13 / DWGSIM
  Whole Genome Simulator for Next-Generation Sequencing
  ☆99Updated 8 months ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆169Updated this week
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆191Updated this week
• zwdzwd / transvar
  TransVar - multiway annotator for precision medicine
  ☆126Updated 2 years ago
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆134Updated 4 years ago
• epi2me-labs / wf-human-variation
  ☆131Updated 2 weeks ago
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆197Updated last week