Alternatives and similar repositories for bedtools:

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

• brentp / bio-playground
  miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
  ☆181Updated 6 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆194Updated 3 years ago
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 2 years ago
• CCDG / Pipeline-Standardization
  ☆82Updated 6 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 2 months ago
• arq5x / bedtools-protocols
  ☆78Updated 10 years ago
• COMBINE-lab / RapMap
  Rapid sensitive and accurate read mapping via quasi-mapping
  ☆89Updated 4 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆191Updated last year
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆155Updated last year
• cc2qe / vawk
  An awk-like VCF parser
  ☆55Updated last year
• jstjohn / SeqPrep
  Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
  ☆142Updated 8 years ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 5 years ago
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆127Updated 3 years ago
• zstephens / neat-genreads
  NEAT read simulation tools
  ☆97Updated 2 years ago
• CGATOxford / cgat
  Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps
  ☆124Updated 6 years ago
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆94Updated 7 months ago
• ExpressionAnalysis / ea-utils
  Automatically exported from code.google.com/p/ea-utils
  ☆95Updated last year
• lh3 / fermi-lite
  Standalone C library for assembling Illumina short reads in small regions
  ☆72Updated 2 years ago
• dnanexus-rnd / GLnexus
  Scalable gVCF merging and joint variant calling for population sequencing projects
  ☆154Updated 9 months ago
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 6 years ago
• alyssafrazee / ballgown
  Bioconductor package "ballgown", devel version. Isoform-level differential expression analysis in R.
  ☆144Updated 3 years ago
• RCollins13 / CNView
  Visualization and annotation of CNVs from population-scale whole-genome sequencing data
  ☆69Updated 7 years ago
• DaehwanKimLab / hisat
  Fast spliced aligner with low memory requirements
  ☆41Updated 9 years ago
• AndersenLab / VCF-kit
  VCF-kit: Assorted utilities for the variant call format
  ☆126Updated 5 months ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆108Updated 4 years ago
• relipmoc / skewer
  ☆94Updated 2 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆110Updated 6 months ago