324 Open source projects that are alternatives of or similar to wgd

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

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

Ten Quick Tips for Deep Learning in Biology

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

Genomic Data Retrieval with R

GenomeTools genome analysis system.

Official git repository for Biopython (originally converted from CVS)

An open-source toolkit for large-scale genomic analysis

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

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

SDK for GPU accelerated genome assembly and analysis

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

A powerful open source data warehouse system

Haplotype VCF comparison tools

Chromosome visualization for the web

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

Rapid large-scale prokaryote pan genome analysis

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

Tools to work with variant call format files

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

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

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

nim wrapper for htslib for parsing genomics data files

Seven Bridges Genomics aligner/caller debugging and analysis tools

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

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

A tool to circularize genome assemblies

Intuitive local web frontend for the BLAST bioinformatics tool

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

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

Configuration tutorials for a variety of mail user agents.

A genome browser that shows long reads and complex variants better

JavaScript VisualizationTools

Deep learning infrastructure for bioinformatics

Find target sites for the miRNAs in genomic sequences

Reads simulator

cython + htslib == fast VCF and BCF processing

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

A Framework for Coalescent Simulation in R

Viral genomics analysis pipelines

An ultrafast memory-efficient short read aligner

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

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

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

Performant Pythonic GenomicRanges

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

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

Bayesian haplotype-based mutation calling

🔬 BEDOPS: high-performance genomic feature operations

MISO: An open-source LIMS for NGS sequencing centres

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

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

Fast large scale matrix visualization for the web.

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

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

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

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

Population assignment analysis using R

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.