Alternatives and similar repositories for pybedtools

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

• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆348Updated 2 weeks ago
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆247Updated last year
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆128Updated 5 years ago
• g2nb / igv-jupyter
  Extension for Jupyter which integrates igv.js
  ☆154Updated 2 years ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆356Updated 7 months ago
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆492Updated last month
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆310Updated last year
• brentp / cyvcf2
  cython + htslib == fast VCF and BCF processing
  ☆421Updated 2 months ago
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆238Updated 11 months ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆329Updated 7 months ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆322Updated 3 years ago
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆261Updated 5 months ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆245Updated 3 years ago
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆429Updated 7 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆262Updated 2 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆557Updated last year
• The-Sequence-Ontology / Specifications
  GFF and GVF specification documents
  ☆216Updated last year
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆301Updated 2 years ago
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆395Updated last month
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆391Updated 3 months ago
• pcingola / SnpEff
  ☆297Updated 2 weeks ago
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆245Updated 4 months ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆290Updated last month
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆322Updated last month
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
  ☆184Updated last week
• AstraZeneca-NGS / VarDict
  VarDict
  ☆201Updated last year
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆395Updated last week
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆195Updated 3 weeks ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆199Updated this week
• macarthur-lab / gene_lists
  List of gene lists for genomic analyses.
  ☆224Updated 3 years ago