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

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

🔬 Assemble large genomes using short reads

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

GenomeTools genome analysis system.

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Official code repository for GATK versions 4 and up

A package for designing compact and comprehensive capture probe sets.

A genome browser that shows long reads and complex variants better

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

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

🌈Scaffold genome sequence assemblies using linked read sequencing data

A cool place to store your Hi-C

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

Bio4j abstract model and general entry point to the project

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

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

Benchmarking programming languages/implementations for common tasks in Bioinformatics

Python module for average nucleotide identity analyses

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

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

SortMeRNA: next-generation sequence filtering and alignment tool

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

APBS - software for biomolecular electrostatics and solvation

Genome annotation with AUGUSTUS

An efficient FASTQ manipulation suite

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

UGENE is free open-source cross-platform bioinformatics software

Simple simulation of single-cell RNA sequencing data

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

Genomic Data Retrieval with R

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

ECG classification programs based on ML/DL methods

pymzML - an interface between Python and mzML Mass spectrometry Files

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

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

A Practical and Efficient NCBI Taxonomy Toolkit

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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.

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

A collection of scripts and notes related to genomics and bioinformatics

R package for analyzing single-cell RNA-seq data

Inference of ploidy and heterozygosity structure using whole genome sequencing data

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

Demonstrating best practices for bioinformatics command line tools

Antimicrobial Resistance Identification By Assembly

Bayesian haplotype-based mutation calling

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

✏️ A versatile DNA sequence optimizer

A DSL for data-driven computational pipelines

Single cell perturbation prediction

GCP Essentials for Bioinformatics Researchers

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

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

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