418 Open source projects that are alternatives of or similar to nPhase

Build and maintain multiple custom conda environments all in once place.

Predict plasmids from uncorrected long read data

Bystro genetic analysis (annotation, filtering, statistics)

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

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Assembling the cause of phenotypes and genotypes from NGS data

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

Real-time species-typing visualisation for nanopore data.

Toolkit for preparing genomes for submission to NCBI

An R package for reproducible and automated ADMIXTOOLS analyses

The Ensembl Compara Perl API and SQL schema

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Streamlining SLAM-seq analysis with ultra-high sensitivity

Computational Analysis of Novel Drug Opportunities

Simple pure Python SAM parser and objects for working with SAM records

A simple command-line tool to download data from Joint Genome Institute databases

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

A modular annotation tool for genomic variants

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

Fast hash function for DNA sequences

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

Multilocus sequence typing by blast using the schemes from PubMLST

GRAph-based Finding of Individual Motif Occurrences

A bioinformatics pipeline to analyze mtDNA from NGS data

Genomics using open source tools, running on GCP or AWS

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

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

Golang for Bioinformatics

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

Improving genome bins through the combination of different binning programs

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

A faster lmm for GWAS. Supports GPU backend.

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

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

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

Genetic maps in autopolyploids

Classify sequencing reads using MinHash.

A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

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

Python toolkit for building restartable pipelines

Single Cell Analysis Pipelines

GREIN : GEO RNA-seq Experiments Interactive Navigator

Open source Java library for computational proteomics

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

A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

Bioinformatics curated workflows that use Biocontainers tools

API for linked biological knowledge

Distribution of TEs and their relationship to genes in host genome

dysgu-SV is a collection of tools for calling structural variants using short or long reads

Improve the quality of a denovo assembly by scaffolding and gap filling

Minor Variant Calling and Phasing Tools

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

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

Finds SNP sites from a multi-FASTA alignment file

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.

The BridgeDb Library source code

<<------ Use SnapATAC!!