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

COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)

📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

pythonic wrapper for htslib

Redis Secondary Indexing Module, been suspended see: https://github.com/RediSearch/RediSearch/

API for linked biological knowledge

Large genome reassembly based on Hi-C data, continuation of GRAAL

SQL Optimizer And Rewriter

The GenePattern Server web application

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

DriverPower

Modular and universal bioinformatics

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Golang for Bioinformatics

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

a pileup library that embraces the huge

libDrive is a Google Drive media library manager and indexer, similar to Plex, that organizes Google Drive media to offer an intuitive and user-friendly experience.

DOM Text Based Multiple Sequence Alignment Library

Per-base per-nucleotide depth analysis

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

A Kotlin DSL and library to create and plot RNA 2D structures

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

simuG: a general-purpose genome simulator

Open source Java library for computational proteomics

Genome-wide imputation pipeline

Detecting methylation using signal-level features from Nanopore sequencing reads of plants

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

An interactive web portal for exploring immuno-oncology data

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

minimalistic nucleic acid folding

A Go package for engineering organisms.

Genomics Workflows on AWS

Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

A tool for fast and accurate summarizing of variant calling format (VCF) files

MMseqs2 app to run on your workstation or servers

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

Streamlining SLAM-seq analysis with ultra-high sensitivity

Inference of switch-like differential expression along single-cell trajectories

Seven Bridges Genomics aligner/caller debugging and analysis tools

An R package for reproducible and automated ADMIXTOOLS analyses

Structural variant and indel caller for mapped sequencing data

waka waka

PERF is an Exhaustive Repeat Finder

exploratory and interactive microbiome analyses based on heatmaps

Clustering scRNAseq by genotypes

Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.

Classify sequencing reads using MinHash.

Genomics data visualization in Python by using matplotlib.

FRP: Fast Random Projections

A proof of concept of RNAseq pipeline

This library tackles the construction and efficient execution of computational chemistry workflows

Curated list of bioinformatics formats and publications

A computational library for learning and evaluating biological knowledge graph embeddings

a fast, real-time file searching program for linux

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

Monorepo with JBrowse 2 web, JBrowse 2 desktop, the JB core package, and core plugins. To customize behaviors, write an in-house plugin.

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.