449 Open source projects that are alternatives of or similar to atropos

Java utilities for Bioinformatics

Official code repository for GATK versions 4 and up

Data intensive science for everyone.

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

A robust model for quantitative comparison of ChIP-Seq data sets.

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

A package for designing compact and comprehensive capture probe sets.

Project metadata manager for PEPs in Python

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

C library for high-throughput sequencing data formats

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

R package for analyzing single-cell RNA-seq data

UGENE is free open-source cross-platform bioinformatics software

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

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

NGLess: NGS with less work

Method to optimally select samples for validation and resequencing

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

A simplified pipeline for ctDNA sequencing data analysis

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Tools to process and analyze deep sequencing data.

(No maintenance) Detect gene fusion directly from raw fastq files

Tools for working with genomic and high throughput sequencing data.

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

GNparser normalises scientific names and extracts their semantic elements.

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

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.

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

Genomics using open source tools, running on GCP or AWS

Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

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

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

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

Toolkit for preparing genomes for submission to NCBI

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

Golang for Bioinformatics

Streamlining SLAM-seq analysis with ultra-high sensitivity

Computational Analysis of Novel Drug Opportunities

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

Improving genome bins through the combination of different binning programs

The Ensembl Compara Perl API and SQL schema

A faster lmm for GWAS. Supports GPU backend.

A set of command line tools based on R and JavaScript.

An R package for reproducible and automated ADMIXTOOLS analyses

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

A simple tool to calculate reads number and total base count in FASTQ file

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

Reference-based transcript discovery from long RNA read

List of IARC bioinformatics nextflow pipelines

Read and write FASTQ and FASTA efficiently from Python

Fast hash function for DNA sequences

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

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

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.

Efficient handling of FASTQ files from Python

Classify sequencing reads using MinHash.

Whole Exome/Whole Genome Sequencing alignment pipeline

A scalable bacterial genome assembly, annotation and analysis pipeline

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