a python package for fast random access to sequences from plain and gzipped FASTA/Q files
☆298Jun 10, 2026Updated 3 months ago
Alternatives and similar repositories for pyfastx
Users that are interested in pyfastx are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Efficient pythonic random access to fasta subsequences☆489Sep 3, 2026Updated 2 weeks ago
- Fast FASTX parsing and k-mer methods in Rust☆215Sep 14, 2026Updated last week
- A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)☆145Aug 24, 2025Updated last year
- Performant Pythonic GenomicRanges☆491Apr 23, 2026Updated 5 months ago
- A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV☆481Jul 15, 2026Updated 2 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Align proteins to genomes with splicing and frameshift☆420Jan 5, 2026Updated 8 months ago
- A cross-platform and ultrafast toolkit for FASTA/Q file manipulation☆1,593Updated this week
- Per-base per-nucleotide depth analysis☆151May 9, 2026Updated 4 months ago
- Genomic interval operations on Pandas DataFrames☆195Sep 7, 2026Updated 2 weeks ago
- Accurate metagenomic profiling && Fast large-scale sequence/genome searching☆222Apr 24, 2026Updated 4 months ago
- Genome browser and variant annotation☆399Aug 24, 2026Updated 3 weeks ago
- Rust bindings to minimap2 library☆113Sep 14, 2026Updated last week
- Python bindings for the TaxonKit library☆43Aug 3, 2026Updated last month
- An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)☆2,430Sep 10, 2026Updated last week
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- FastRemap, a C++ tool for quickly remapping reads between genome assemblies based on the commonly used CrossMap tool. Link to paper: http…☆26Aug 24, 2022Updated 4 years ago
- A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.☆25Nov 25, 2025Updated 9 months ago
- Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!☆189Mar 17, 2026Updated 6 months ago
- Download FASTQ files from SRA or ENA repositories.☆405May 16, 2026Updated 4 months ago
- 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…☆911Sep 7, 2026Updated 2 weeks ago
- base-accurate DNA sequence alignments using WFA and mashmap3☆224Aug 27, 2026Updated 3 weeks ago
- PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.☆29Aug 20, 2025Updated last year
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,249May 19, 2026Updated 4 months ago
- An accurate GFF3/GTF lift over pipeline☆557Aug 1, 2023Updated 3 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆877May 2, 2026Updated 4 months ago
- An ultra-fast and efficient genomic tool for coverage calculation☆175Jun 9, 2026Updated 3 months ago
- CLI tool for querying the Genome Taxonomy Database (GTDB). Batch search, genome cards, taxon lineages, and cross-release taxonomic compar…☆33Updated this week
- Package for fetching metadata and downloading data from SRA/ENA/GEO☆369Aug 16, 2026Updated last month
- Structural variant toolkit for VCFs☆423Updated this week
- seqfu - Sequece Fastx Utilities☆131Updated this week
- Plot structural variant signals from many BAMs and CRAMs☆573Jul 13, 2024Updated 2 years ago
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆20Sep 1, 2026Updated 3 weeks ago
- Robust individual and aggregate checksums for nucleotide sequences☆18Mar 3, 2026Updated 6 months ago
- 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.
- A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster to…☆190Aug 28, 2026Updated 3 weeks ago
- Aligns short reads using dynamic seed size with strobemers☆207Updated this week
- A lightweight library for working with PAF (Pairwise mApping Format) files☆31May 25, 2026Updated 3 months ago
- A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …☆197Sep 1, 2026Updated 3 weeks ago
- A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆53May 5, 2026Updated 4 months ago
- A grammar of graphics for comparative genomics☆782Sep 2, 2026Updated 3 weeks ago
- LexicMap: efficient sequence alignment against millions of prokaryotic genomes☆227Sep 15, 2026Updated last week