Alternatives and similar repositories for bedtools

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

• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 3 years ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆110Updated 5 years ago
• brentp / bio-playground
  miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
  ☆182Updated 7 years ago
• zstephens / neat-genreads
  NEAT read simulation tools
  ☆101Updated 3 years ago
• jstjohn / SeqPrep
  Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
  ☆145Updated 9 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆117Updated last year
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆204Updated 4 years ago
• andyrimmer / Platypus
  Platypus Variant Caller
  ☆108Updated last year
• mozack / abra2
  ABRA2
  ☆95Updated 3 years ago
• COMBINE-lab / RapMap
  Rapid sensitive and accurate read mapping via quasi-mapping
  ☆90Updated 5 years ago
• PacificBiosciences / DevNet
  The DevNet project on github stores the PacBio DevNet website.
  ☆115Updated 7 years ago
• relipmoc / skewer
  ☆96Updated 3 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆201Updated 2 years ago
• CCDG / Pipeline-Standardization
  ☆81Updated 7 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• svviz / svviz
  Read visualizer for structural variants
  ☆84Updated 7 years ago
• gt1 / biobambam2
  Tools for early stage alignment file processing
  ☆95Updated 6 years ago
• nh13 / DWGSIM
  Whole Genome Simulator for Next-Generation Sequencing
  ☆102Updated last month
• RCollins13 / CNView
  Visualization and annotation of CNVs from population-scale whole-genome sequencing data
  ☆72Updated 8 years ago
• smithlabcode / preseq
  Software for predicting library complexity and genome coverage in high-throughput sequencing.
  ☆94Updated last month
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆103Updated 5 years ago
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆136Updated 4 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆165Updated 2 years ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆151Updated 2 weeks ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated last year
• parklab / bamsnap
  ☆122Updated 6 months ago
• Czh3 / NGSTools
  Next-Generation Sequencing(NGS) toolkits.
  ☆48Updated 9 years ago
• davetang / learning_bam_file
  Learning the Sequence Alignment/Map format
  ☆112Updated 6 months ago
• genome-in-a-bottle / giab_latest_release
  This repository contains information about latest release from Genome in a Bottle project
  ☆75Updated 6 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆99Updated 3 years ago