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

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

A curated list of awesome Bioinformatics libraries and software.

Application for making ENCODE Blacklists

Post-analysis of immune repertoire sequencing data

Next generation sequencing reads de novo assembler.

Bioinformatics Workbook repository

dna2vec: Consistent vector representations of variable-length k-mers

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

SortMeRNA: next-generation sequence filtering and alignment tool

A method for variant graph genotyping based on exact alignment of k-mers

SquiggleKit: A toolkit for manipulating nanopore signal data

APBS - software for biomolecular electrostatics and solvation

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

The sources of the openSNP website

Bayesian genotyper for structural variants

An efficient FASTQ manipulation suite

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

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:

A fast whole-genome aligner based on de Bruijn graphs

Parser and database to index the terpene profile of different strains of Cannabis from online databases

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

A tutorial on methods of 16S analysis with QIIME 1

Robust and efficient workflows using a simple language agnostic approach

Benchmarking programming languages/implementations for common tasks in Bioinformatics

Flexible genotype query among 30,000+ samples whole-genome

nim wrapper for htslib for parsing genomics data files

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

compacted de Bruijn graph construction in low memory

RNA-seq workflow using STAR and DESeq2

🌈Scaffold genome sequence assemblies using linked read sequencing data

A Practical and Efficient NCBI Taxonomy Toolkit

Genome inference from a population reference graph

Simple simulation of single-cell RNA sequencing data

ABRA2

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

LAMBDA – the Local Aligner for Massive Biological DatA

Package for fetching metadata and downloading data from SRA/ENA/GEO

Model and predict short DNA sequence features with neural networks

A collection of scripts and notes related to genomics and bioinformatics

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

A library for generating an interactive SVG visualization of CWL workflows

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

pymzML - an interface between Python and mzML Mass spectrometry Files

Python Programming for Biologists

Support Vector Structural Variation Genotyper

Sequana: a set of Snakemake NGS pipelines

Emperor a tool for the analysis and visualization of large microbial ecology datasets

Yet Another Chimeric Read Detector

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

A curated list of bioinformatics bench-marking papers and resources.

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Analysis pipelines for sequencing data

Demonstrating best practices for bioinformatics command line tools

Lightweight Iterative Gene set Enrichment in R

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing