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

Genome Annotation Without Nightmares

Viral genomics analysis pipelines

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

structural variant calling and genotyping with existing tools, but, smoothly.

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

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

Seven Bridges Genomics aligner/caller debugging and analysis tools

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

Phage-Host Interaction Search Tool

Bayesian haplotype-based mutation calling

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

MISO: An open-source LIMS for NGS sequencing centres

DriverPower

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

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

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

High-performance error correction for Illumina resequencing data

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

JavaScript VisualizationTools

An R package for creating Q-Q and manhattan plots from GWAS results

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

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

cython + htslib == fast VCF and BCF processing

Simulate genealogical trees and genomic sequence data using population genetic models

Easy genetic ancestry predictions in Python

Inference of ploidy and heterozygosity structure using whole genome sequencing data

An ultrafast memory-efficient short read aligner

AQUAS TF and histone ChIP-seq pipeline

use the noise

Bioinformatics library for .NET

Performant Pythonic GenomicRanges

Dynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features

Python package and CLI for whole-genome duplication related analyses

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

🔬 BEDOPS: high-performance genomic feature operations

Bayesian genotyper for structural variants

Finds SNP sites from a multi-FASTA alignment file

An interactive web tool for quality control of DNA sequencing data

Fast large scale matrix visualization for the web.

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

Population assignment analysis using R

A collaboratively written review paper on deep learning, genomics, and precision medicine

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

Development repository for the Bioconductor package 'mixOmics '

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Framework for building fast genomics web tools with WebAssembly and WebWorkers

Intuitive local web frontend for the BLAST bioinformatics tool

Guided synteny alignment between duplicated genomes (within specified quota constraint)

A multi-thread implementation of node2vec random walk.

igv.js server and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

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

RADseq Data Exploration, Manipulation and Visualization using R

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

A genome browser that shows long reads and complex variants better

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

Ten Quick Tips for Deep Learning in Biology