Alternatives and similar repositories for scikit-allel

Users that are interested in scikit-allel are comparing it to the libraries listed below

• sgkit-dev / sgkit
  Scalable genetics toolkit
  ☆273Updated 4 months ago
• brentp / cyvcf2
  cython + htslib == fast VCF and BCF processing
  ☆427Updated 3 months ago
• daler / pybedtools
  Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
  ☆328Updated 10 months ago
• g2nb / igv-jupyter
  Extension for Jupyter which integrates igv.js
  ☆154Updated 3 years ago
• GangCaoLab / CoolBox
  Jupyter notebook based genomic data visualization toolkit.
  ☆249Updated 2 months ago
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆493Updated last week
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆314Updated last week
• vanheeringen-lab / genomepy
  genes and genomes at your fingertips
  ☆406Updated 4 months ago
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆323Updated this week
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆129Updated 5 years ago
• lmdu / pyfastx
  a python package for fast random access to sequences from plain and gzipped FASTA/Q files
  ☆289Updated 3 weeks ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆359Updated 9 months ago
• mdshw5 / pyfaidx
  Efficient pythonic random access to fasta subsequences
  ☆482Updated 5 months ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆331Updated 8 months ago
• gosling-lang / gos
  A declarative interactive genomics visualization library for Python.
  ☆234Updated 2 months ago
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆398Updated this 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 this week
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆429Updated 8 months ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆348Updated last month
• The-Sequence-Ontology / Specifications
  GFF and GVF specification documents
  ☆219Updated last year
• bxlab / bx-python
  Tools for manipulating biological data, particularly multiple sequence alignments
  ☆159Updated last week
• bcgsc / NanoSim
  Nanopore sequence read simulator
  ☆287Updated this week
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆247Updated last year
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆337Updated 3 years ago
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆212Updated 5 years ago
• jeetsukumaran / DendroPy
  A Python library for phylogenetic scripting, simulation, data processing and manipulation.
  ☆229Updated 3 weeks ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆558Updated last year
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆323Updated 4 years ago
• pcingola / SnpEff
  ☆302Updated last week
• konstantint / pyliftover
  Pure-python implementation of UCSC liftOver genome coordinate conversion
  ☆101Updated last year