447 Open source projects that are alternatives of or similar to Fgbio

SquiggleKit: A toolkit for manipulating nanopore signal data

Mulled - Automatized Containerized Software Repository

DEPRECIATED! Please use nf-core/tools instead

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

APBS - software for biomolecular electrostatics and solvation

MView extracts and reformats the results of a sequence database search or multiple alignment.

A Python package for fast operations on 1-dimensional genomic signal tracks

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

Version 5 of the CAFE phylogenetics software

Estimation of pairwise distances under a probabilistic framework

The sources of the openSNP website

🎯 Human transcription factor target genes.

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

Bayesian genotyper for structural variants

MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

Curated list of bioinformatics formats and publications

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Aggregate results from bioinformatics analyses across many samples into a single report.

Scalable long read self-correction and assembly polishing with multiple sequence alignment

An efficient FASTQ manipulation suite

Fast hash function for DNA sequences

A plotly.js React component from Plotly 📈

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

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

Golang for Bioinformatics

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

Simple pure Python SAM parser and objects for working with SAM records

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

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

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

A fast whole-genome aligner based on de Bruijn graphs

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

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

Streamlining SLAM-seq analysis with ultra-high sensitivity

An R package for reproducible and automated ADMIXTOOLS analyses

Race and ethnicity Imputation from Disease history with Deep LEarning

Build and maintain multiple custom conda environments all in once place.

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

Provides access to complex Bioinformatics software (even BioLinux!) in just one command.

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Biostar Q&A

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

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Robust and efficient workflows using a simple language agnostic approach

Earl Grey: A fully automated TE curation and annotation pipeline

GNparser normalises scientific names and extracts their semantic elements.

Versatile open-source tool for microbiome analysis

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

Benchmarking programming languages/implementations for common tasks in Bioinformatics

Comprehensive toolkit for generating various numerical features of protein sequences

No description or website provided.

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

Workflow Description Language - Specification and Implementations

Syntax highlighting for computational biology

Fast Reference-Guided Scaffolding of Genome Assembly Contigs. RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag

BioGrakn Knowledge Graph

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Code examples of fast and simple k-mer counters for tutorial purposes