Alternatives and similar repositories for bedtools:

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

• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆131Updated 4 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆196Updated 4 years ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆108Updated 4 years ago
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆158Updated 2 years ago
• brentp / bio-playground
  miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
  ☆182Updated 6 years ago
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 2 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• COMBINE-lab / RapMap
  Rapid sensitive and accurate read mapping via quasi-mapping
  ☆89Updated 4 years ago
• lh3 / bgt
  Flexible genotype query among 30,000+ samples whole-genome
  ☆96Updated 5 years ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆151Updated 3 years ago
• Czh3 / NGSTools
  Next-Generation Sequencing(NGS) toolkits.
  ☆45Updated 9 years ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆250Updated 10 months ago
• relipmoc / skewer
  ☆94Updated 2 years ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 5 years ago
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆97Updated 11 months ago
• RCollins13 / CNView
  Visualization and annotation of CNVs from population-scale whole-genome sequencing data
  ☆71Updated 7 years ago
• CCDG / Pipeline-Standardization
  ☆82Updated 6 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆114Updated 9 months ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆140Updated 3 weeks ago
• PacificBiosciences / DevNet
  The DevNet project on github stores the PacBio DevNet website.
  ☆116Updated 6 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆105Updated 4 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 6 months ago
• ComparativeGenomicsToolkit / hal
  Hierarchical Alignment Format
  ☆168Updated 4 months ago
• svviz / svviz
  Read visualizer for structural variants
  ☆83Updated 6 years ago
• zstephens / neat-genreads
  NEAT read simulation tools
  ☆98Updated 2 years ago
• Kingsford-Group / scallop
  Scallop is a reference-based transcriptome assembler for RNA-seq
  ☆90Updated 4 years ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆87Updated 7 months ago
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 6 years ago