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
  ☆264Updated last week
• brentp / cyvcf2
  cython + htslib == fast VCF and BCF processing
  ☆414Updated last week
• daler / pybedtools
  Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
  ☆326Updated 6 months ago
• mdshw5 / pyfaidx
  Efficient pythonic random access to fasta subsequences
  ☆479Updated last month
• g2nb / igv-jupyter
  Extension for Jupyter which integrates igv.js
  ☆154Updated 2 years ago
• snakemake / snakemake-wrappers
  This is the development home of the Snakemake wrapper repository, see
  ☆232Updated last week
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆308Updated last year
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆318Updated last week
• lmdu / pyfastx
  a python package for fast random access to sequences from plain and gzipped FASTA/Q files
  ☆289Updated 9 months ago
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆489Updated 2 weeks ago
• vanheeringen-lab / genomepy
  genes and genomes at your fingertips
  ☆400Updated last week
• bioconvert / bioconvert
  Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
  ☆382Updated 3 months ago
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆194Updated last week
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆351Updated 5 months ago
• bxlab / bx-python
  Tools for manipulating biological data, particularly multiple sequence alignments
  ☆158Updated 2 weeks ago
• GangCaoLab / CoolBox
  Jupyter notebook based genomic data visualization toolkit.
  ☆247Updated 6 months ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆341Updated last week
• gosling-lang / gos
  A declarative interactive genomics visualization library for Python.
  ☆229Updated last month
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆552Updated last year
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆379Updated 2 weeks 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.
  ☆222Updated 3 months ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆326Updated 4 months ago
• The-Sequence-Ontology / Specifications
  GFF and GVF specification documents
  ☆215Updated last year
• HadrienG / InSilicoSeq
  A sequencing simulator
  ☆208Updated 3 months ago
• lh3 / readfq
  Fast multi-line FASTA/Q reader in several programming languages
  ☆176Updated 4 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆318Updated 3 years ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆257Updated last year
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆333Updated 3 years ago
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆127Updated 5 years ago