423 Open source projects that are alternatives of or similar to Soapdenovo2

Genome annotation with AUGUSTUS

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

An efficient FASTQ manipulation suite

EDAM is an ontology of bioinformatics types of data including identifiers, data formats, operations and topics.

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

Bayesian genotyper for structural variants

UGENE is free open-source cross-platform bioinformatics software

Biological sequences for the julia language

Simple simulation of single-cell RNA sequencing data

An interactive web tool for quality control of DNA sequencing data

Benchmarking programming languages/implementations for common tasks in Bioinformatics

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

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 tool to circularize genome assemblies

Race and ethnicity Imputation from Disease history with Deep LEarning

GeneValidator: Identify problems with predicted genes

The START App: R Shiny Transcriptome Analysis Resource Tool

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

Solutions to assignments of Coursera Specializations - Deep learning, Machine learning, Algorithms & Data Structures, Image Processing and Python For Everybody

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

Global Biotic Interactions provides access to existing species interaction datasets

A Practical and Efficient NCBI Taxonomy Toolkit

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

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.

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

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

A tutorial on methods of 16S analysis with QIIME 1

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

R package for analyzing single-cell RNA-seq data

Python Programming for Biologists

Inference of ploidy and heterozygosity structure using whole genome sequencing data

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

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

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

Antimicrobial Resistance Identification By Assembly

Lightweight Iterative Gene set Enrichment in R

Bayesian haplotype-based mutation calling

Tools and databases for analyzing HLA and VDJ genes.

A DSL for data-driven computational pipelines

Single cell perturbation prediction

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

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

Exact Tandem Repeat Finder (not a TRF replacement)

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

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Bioinformatics library for .NET

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

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

Application for making ENCODE Blacklists

Genomics Extension for SQLite

Comprehensive toolkit for generating various numerical features of protein sequences

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

A robust and fast clustering method for amplicon-based studies

Using artificial intelligence and genetic algorithms to automatically write programs. Tutorial: http://www.primaryobjects.com/cms/article149

Snakemake-based workflow for detecting structural variants in WGS data

A comprehensive library for computational molecular biology

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

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