284 Open source projects that are alternatives of or similar to mity

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

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

🔬 BEDOPS: high-performance genomic feature operations

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

An ultrafast memory-efficient short read aligner

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

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

Genome-wide imputation pipeline

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

Deep learning infrastructure for bioinformatics

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

cython + htslib == fast VCF and BCF processing

Genomics Workflows on AWS

Performant Pythonic GenomicRanges

simuG: a general-purpose genome simulator

Fast large scale matrix visualization for the web.

A python and C++ library for reading and writing neuronal morphologies

Intuitive local web frontend for the BLAST bioinformatics tool

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

A genome browser that shows long reads and complex variants better

Seven Bridges Genomics aligner/caller debugging and analysis tools

Reads simulator

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

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

Viral genomics analysis pipelines

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

Official git repository for Biopython (originally converted from CVS)

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

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

Phage-Host Interaction Search Tool

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

Find target sites for the miRNAs in genomic sequences

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

Collection of scripts for bacterial genomics

SDK for GPU accelerated genome assembly and analysis

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

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

High-performance error correction for Illumina resequencing data

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

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

A powerful open source data warehouse system

a pileup library that embraces the huge

GenomeTools genome analysis system.

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

Chromosome visualization for the web

Easy genetic ancestry predictions in Python

Ten Quick Tips for Deep Learning in Biology

Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)

Rapid large-scale prokaryote pan genome analysis

Genome Annotation Without Nightmares

An open-source toolkit for large-scale genomic analysis

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

Tools to work with variant call format files

Python package and CLI for whole-genome duplication related analyses

Genomic Data Retrieval with R

Haplotype VCF comparison tools

BACTpipe: An assembly and annotation pipeline for bacterial genomics

Finds SNP sites from a multi-FASTA alignment file

Biopython Jupyter Notebook tutorial to characterize a small genome

Population assignment analysis using R