Alternatives and similar repositories for pybedtools

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

• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆351Updated 4 months ago
• brentp / cyvcf2
  cython + htslib == fast VCF and BCF processing
  ☆412Updated this week
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆244Updated 10 months ago
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆125Updated 5 years ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆339Updated 3 weeks ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆243Updated 2 years ago
• g2nb / igv-jupyter
  Extension for Jupyter which integrates igv.js
  ☆154Updated 2 years ago
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆429Updated 3 months ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆317Updated 3 years ago
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆233Updated 7 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆258Updated 2 years ago
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆484Updated 6 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆545Updated last year
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆325Updated 3 months ago
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆306Updated last year
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆383Updated 2 weeks ago
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆377Updated 3 months ago
• The-Sequence-Ontology / Specifications
  GFF and GVF specification documents
  ☆214Updated last year
• pcingola / SnpEff
  ☆290Updated last week
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆199Updated last month
• macarthur-lab / gene_lists
  List of gene lists for genomic analyses.
  ☆222Updated 3 years ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆297Updated 2 years ago
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆256Updated last month
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated 2 weeks ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆280Updated last year
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆398Updated last month
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆381Updated 3 years ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆262Updated this week
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆203Updated last year