398 Open source projects that are alternatives of or similar to Parallel Fastq Dump

pymzML - an interface between Python and mzML Mass spectrometry Files

Race and ethnicity Imputation from Disease history with Deep LEarning

NGLess: NGS with less work

SortMeRNA: next-generation sequence filtering and alignment tool

Post-analysis of immune repertoire sequencing data

A tool to circularize genome assemblies

✏️ A versatile DNA sequence optimizer

MOLGENIS - for scientific data: management, exploration, integration and analysis.

Bio4j abstract model and general entry point to the project

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

Conda recipes for the bioconda channel.

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

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

Fast multi-line FASTA/Q reader in several programming languages

Demonstrating best practices for bioinformatics command line tools

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

GCP Essentials for Bioinformatics Researchers

Bayesian haplotype-based mutation calling

Genomics Extension for SQLite

A cool place to store your Hi-C

A curated list of awesome Bioinformatics libraries and software.

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

Bioinformatics Workbook repository

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

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

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

A Practical and Efficient NCBI Taxonomy Toolkit

nim wrapper for htslib for parsing genomics data files

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.

Single cell perturbation prediction

A collection of scripts and notes related to genomics and bioinformatics

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

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Application for making ENCODE Blacklists

Antimicrobial Resistance Identification By Assembly

Simple simulation of single-cell RNA sequencing data

A DSL for data-driven computational pipelines

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

FastQC port to Qt5: A quality control tool for high throughput sequence data.

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

Bioinformatics library for .NET

APBS - software for biomolecular electrostatics and solvation

A robust and fast clustering method for amplicon-based studies

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

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

An efficient FASTQ manipulation suite

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

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:

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

UGENE is free open-source cross-platform bioinformatics software

Structural variant toolkit for VCFs

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

Benchmarking programming languages/implementations for common tasks in Bioinformatics

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

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A comprehensive library for computational molecular biology

ECG classification programs based on ML/DL methods

Python module for average nucleotide identity analyses