300 Open source projects that are alternatives of or similar to mandrake

Some Cool NLP and CV Repositories and Solutions （收集NLP中常见任务的开源解决方案、数据集、工具、学习资料等）

A Java API for high-throughput sequencing data (HTS) formats.

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

simuG: a general-purpose genome simulator

Official git repository for Biopython (originally converted from CVS)

a pileup library that embraces the huge

SDK for GPU accelerated genome assembly and analysis

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

GenomeTools genome analysis system.

Biopython Jupyter Notebook tutorial to characterize a small genome

xHLA: Fast and accurate HLA typing from short read sequence data

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

Haplotype VCF comparison tools

Genome-wide imputation pipeline

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

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

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

Position embedding layers in Keras

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

Collection of scripts for bacterial genomics

A powerful open source data warehouse system

Genomics Workflows on AWS

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

A genome browser that shows long reads and complex variants better

Genome Annotation Without Nightmares

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Seven Bridges Genomics aligner/caller debugging and analysis tools

Phage-Host Interaction Search Tool

A WGS de novo assembler based on the FMD-index for large genomes

DriverPower

A DNA Sequence Alignment/Map (SAM) library for Clojure

High-performance error correction for Illumina resequencing data

JavaScript VisualizationTools

*SEM 2018: Learning Distributed Event Representations with a Multi-Task Approach

cython + htslib == fast VCF and BCF processing

Easy genetic ancestry predictions in Python

An ultrafast memory-efficient short read aligner

use the noise

Performant Pythonic GenomicRanges

Python package and CLI for whole-genome duplication related analyses

🔬 BEDOPS: high-performance genomic feature operations

Finds SNP sites from a multi-FASTA alignment file

Fast large scale matrix visualization for the web.

Population assignment analysis using R

Proof-of-concept seq-to-graph mapper and graph generator

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Intuitive local web frontend for the BLAST bioinformatics tool

A multi-thread implementation of node2vec random walk.

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

Performs memory-efficient reservoir sampling on very large input files delimited by newlines

Find target sites for the miRNAs in genomic sequences

Large genome reassembly based on Hi-C data, continuation of GRAAL

The GenePattern Server web application

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

PyTorch implementation of Deep Randomized Ensembles for Metric Learning(ECCV2018)

A tool for fast and accurate summarizing of variant calling format (VCF) files