398 Open source projects that are alternatives of or similar to Quast

DEPRECIATED! Please use nf-core/tools instead

A curated list of resources for machine learning for small-molecule drug discovery

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

Version 5 of the CAFE phylogenetics software

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

Feature extraction algorithm for genomic data

Bioinformatics Workbook repository

🎯 Human transcription factor target genes.

Robust, flexible and resource-efficient pipelines using Go and the commandline

Ploidy agnostic phasing pipeline and algorithm

Curated (meta)list of resources for Biology.

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

Toolkit for processing sequences in FASTA/Q formats

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

Conda recipes for the bioconda channel.

API for linked biological knowledge

Scalable genomic data analysis.

Golang for Bioinformatics

A tool to circularize genome assemblies

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

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

Open source Java library for computational proteomics

SquiggleKit: A toolkit for manipulating nanopore signal data

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources

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

Improving genome bins through the combination of different binning programs

Unix, R and python tools for genomics and data science

📊 Codon usage tables in code-friendly format + Python bindings

GO enrichment with python -- pandas meets networkx

Classify sequencing reads using MinHash.

List of Computer Science courses with video lectures.

Single Cell Analysis Pipelines

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

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.

Scripts to download genomes from the NCBI FTP servers

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

MyGene.info: A BioThings API for gene annotations

A permissively licensed library designed to replace Illumina's Experiment Manager

BWK awk modified for biological data

Genomics using open source tools, running on GCP or AWS

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

R mased batch sequence downloader, with primer development and in silico evaluation capabilities

Tools to process and analyze deep sequencing data.

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

A fast whole-genome aligner based on de Bruijn graphs

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

MMseqs2: ultra fast and sensitive search and clustering suite

A faster lmm for GWAS. Supports GPU backend.

NGLess: NGS with less work

d3 library to build circular graphs

Rapid large-scale prokaryote pan genome analysis

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Next generation sequencing reads de novo assembler.

Simple simulation of single-cell RNA sequencing data

Antimicrobial Resistance Identification By Assembly

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Project metadata manager for PEPs in Python