Efficient pythonic random access to fasta subsequences
☆486Mar 19, 2026Updated 2 months ago
Alternatives and similar repositories for pyfaidx
Users that are interested in pyfaidx are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- a python package for fast random access to sequences from plain and gzipped FASTA/Q files☆295Updated this week
- Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight…☆894Jun 3, 2026Updated last week
- cython + htslib == fast VCF and BCF processing☆445May 14, 2026Updated last month
- Simple FASTQ quality assessment using Python☆109Feb 24, 2026Updated 3 months ago
- Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")☆330Mar 16, 2025Updated last year
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Performant Pythonic GenomicRanges☆495Apr 23, 2026Updated last month
- Simple pure Python SAM parser and objects for working with SAM records☆64Mar 20, 2026Updated 2 months ago
- Tools to process and analyze deep sequencing data.☆761Jul 23, 2025Updated 10 months ago
- genes and genomes at your fingertips☆413Mar 5, 2026Updated 3 months ago
- Aggregate results from bioinformatics analyses across many samples into a single report.☆1,459May 20, 2026Updated 3 weeks ago
- Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl☆401May 13, 2026Updated last month
- BEDOPS: high-performance genomic feature operations☆369Apr 29, 2025Updated last year
- GFF and GTF file manipulation and interconversion☆319Mar 31, 2026Updated 2 months ago
- Tools for working with SAM/BAM data☆610Dec 22, 2024Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Quickly search, compare, and analyze genomic and metagenomic data sets.☆546Updated this week
- annotate a VCF with other VCFs/BEDs/tabixed files☆407May 1, 2026Updated last month
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,197May 19, 2026Updated 3 weeks ago
- Python library to handle Gene Ontology (GO) terms☆894May 12, 2026Updated last month
- python module to plot beautiful and highly customizable genome browser tracks☆887Jul 10, 2024Updated last year
- A C library for handling bigWig files☆81Jan 17, 2025Updated last year
- fast, memory-efficient, pythonic (and command-line) access to fasta sequence files☆86Dec 11, 2017Updated 8 years ago
- Genomic interval operations on Pandas DataFrames☆191Jun 1, 2026Updated last week
- Python library to plot DNA sequence features (e.g. from Genbank files)☆690Jul 2, 2025Updated 11 months ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆144Aug 24, 2025Updated 9 months ago
- A Python package for exploring and analysing genetic variation data☆316Jun 1, 2026Updated last week
- Efficient handling of FASTQ files from Python☆51Nov 28, 2025Updated 6 months ago
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆680Mar 20, 2026Updated 2 months ago
- Bayesian haplotype-based mutation calling☆323Feb 13, 2026Updated 4 months ago
- A Variant Call Format reader for Python.☆419Sep 22, 2023Updated 2 years ago
- Plot structural variant signals from many BAMs and CRAMs☆567Jul 13, 2024Updated last year
- don't get DUP'ed or DEL'ed by your putative SVs.☆108Dec 14, 2020Updated 5 years ago
- A python extension for quick access to bigWig and bigBed files☆244Jan 14, 2026Updated 5 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Graph-based alignment (Hierarchical Graph FM index)☆540Jan 27, 2026Updated 4 months ago
- Toolkit for processing sequences in FASTA/Q formats☆1,542Jun 1, 2025Updated last year
- An efficient CLI to extract sequences from the SRA☆122Updated this week
- A versatile toolkit for k-mers with taxonomic information☆82Aug 28, 2025Updated 9 months ago
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆858May 2, 2026Updated last month
- Standalone C library for assembling Illumina short reads in small regions☆72Dec 15, 2022Updated 3 years ago
- Python and C++ code for reading and writing genomics data.☆800Dec 9, 2021Updated 4 years ago