Alternatives and similar repositories for bamtools

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

• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆319Updated 3 years ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆328Updated 5 months ago
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆317Updated 3 years ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆491Updated 2 weeks ago
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆248Updated last year
• lh3 / wgsim
  Reads simulator
  ☆282Updated 4 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆200Updated last year
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆389Updated 2 months ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆354Updated 6 months ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆387Updated 3 years ago
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆319Updated last month
• pcingola / SnpEff
  ☆294Updated 2 months ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆165Updated 2 years ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆449Updated last year
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆555Updated last year
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆230Updated 3 years ago
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆213Updated 5 years ago
• brentp / cyvcf2
  cython + htslib == fast VCF and BCF processing
  ☆415Updated last month
• genome-in-a-bottle / giab_data_indexes
  This repository contains data indexes from NIST's Genome in a Bottle project.
  ☆258Updated last year
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆260Updated 2 years ago
• GregoryFaust / samblaster
  samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
  ☆235Updated 4 years ago
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆334Updated 3 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆202Updated 4 years ago
• genome / pindel
  Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …
  ☆174Updated 5 years ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆206Updated 4 years ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆279Updated 5 months ago
• ENCODE-DCC / kentUtils
  UCSC command line bioinformatic utilities
  ☆185Updated last year
• daler / pybedtools
  Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
  ☆327Updated 8 months ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆249Updated 2 months ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆267Updated last month