669 Open source projects that are alternatives of or similar to Pyfaidx

Analysis pipelines for sequencing data

Data intensive science for everyone.

Official git repository for Biopython (originally converted from CVS)

Python and C++ code for reading and writing genomics data.

A package for designing compact and comprehensive capture probe sets.

A fast 23andMe genome text file parser, now superseded by arv

A curated list of awesome bioinformatics software.

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Official code repository for GATK versions 4 and up

A collection of scripts and notes related to genomics and bioinformatics

Proof-of-concept seq-to-graph mapper and graph generator

Intuitive local web frontend for the BLAST bioinformatics tool

An open source platform for managing and analyzing biomedical big data

cython + htslib == fast VCF and BCF processing

🔬 BEDOPS: high-performance genomic feature operations

JavaScript VisualizationTools

Haplotype VCF comparison tools

A package for designing activity-informed nucleic acid diagnostics for viruses.

A simple command-line tool to download data from Joint Genome Institute databases

Example client programs for Saphetor's VarSome annotation API

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

dysgu-SV is a collection of tools for calling structural variants using short or long reads

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

A powerful open source data warehouse system

BACNET is a Java based platform to develop website for multi-omics analysis

GenomeTools genome analysis system.

Compute N50/NG50 and auN/auNG

A high-performance, Pythonic language for bioinformatics

An ultrafast memory-efficient short read aligner

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

A genome browser that shows long reads and complex variants better

Numerical Encoding for Human Genetic Variants

Ultrafast sequence typing and gene detection from NGS raw reads

A faster lmm for GWAS. Supports GPU backend.

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Toolkit for preparing genomes for submission to NCBI

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

Deep learning infrastructure for bioinformatics

De novo assembly based variant calling pipeline for Illumina short reads

An open-access bioinformatics text

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Fast and flexible ORF finder

Bystro genetic analysis (annotation, filtering, statistics)

Fast hash function for DNA sequences

Assembling the cause of phenotypes and genotypes from NGS data

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

Provide R access to the NCI Genomic Data Commons portal.

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

Earl Grey: A fully automated TE curation and annotation pipeline

Fast alignment and preprocessing of chromatin profiles

A React web application to query and share any PostgreSQL database.

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

A comprehensive tutorial about GWAS and PRS

Reads simulator