Top 23 Genomic Open-Source Projects

• Biopython

  31 4,171 9.6 Python

  Official git repository for Biopython (originally converted from CVS)

  

Project mention: Invitación a proyecto - Biopython en Español | /r/devsarg | 2023-07-23

• deepvariant

  5 3,078 9.1 Python

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

  

Project mention: Look over my purchase, is there anything I should return? | /r/buildapc | 2023-05-06

• InfluxDB

  www.influxdata.com featured

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

• minimap2

  5 1,688 7.6 C

  A versatile pairwise aligner for genomic and spliced nucleotide sequences

Project mention: Ask HN: Comment here about whatever you're passionate about at the moment | news.ycombinator.com | 2023-11-06

Interested as well! But the future is not so dark, things like e.g. https://github.com/lh3/minimap2 are a breath of fresh air.

• bwa

  3 1,453 2.7 C

  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Project mention: my friend showed me his code, thees are all functions | /r/ProgrammerHumor | 2023-05-25

Check out these sweet macros (from the same repo): https://github.com/lh3/bwa/blob/139f68fc4c3747813783a488aef2adc86626b01b/kbtree.h

• galaxy

  4 1,315 10.0 Python

  Data intensive science for everyone.

  

Project mention: Need for GUIs for bioinformatic tools? | /r/bioinformatics | 2023-06-17

Maybe it would help you to look at the galaxy project: GitHub main site

• vg

  2 1,061 9.4 C++

  tools for working with genome variation graphs (by vgteam)

  

• adam

  3 967 6.1 Scala

  ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

  

• SaaSHub

  www.saashub.com featured

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• Hail

  5 935 9.8 Python

  Cloud-native genomic dataframes and batch computing

  

• ncbi-genome-download

  4 890 5.7 Python

  Scripts to download genomes from the NCBI FTP servers

• goatools

  2 727 5.0 Python

  Python library to handle Gene Ontology (GO) terms

• bwa-mem2

  2 677 2.6 C++

  The next version of bwa-mem

  

• bowtie2

  2 619 7.4 C++

  A fast and sensitive gapped read aligner

Project mention: NHI Genome Studies: Mexico Govt Sept 12 Congressional hearing | /r/genetics | 2023-09-14

2) Use bowtie2 to align reads against CHM13. This will let you separate human from nonhuman (important, as human sequences are a common contaminant in many nonhuman genomes).

• pyCirclize

  6 610 8.6 Python

  Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

• Vcflib

  0 596 8.0 C++

  C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

  

• BioJava

  2 575 8.2 Java

  :book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

  

Project mention: Outperforming Rust DNA sequence parsing benchmarks by 50% with Mojo | news.ycombinator.com | 2024-02-08

Here is a cache of valid and invalid FASTQ files for unit tests

https://github.com/biojava/biojava/tree/master/biojava-genom...

• megahit

  1 558 0.0 C++

  Ultra-fast and memory-efficient (meta-)genome assembler

• eggnog-mapper

  1 531 4.3 Python

  Fast genome-wide functional annotation through orthology assignment

  

• jvarkit

  1 467 8.9 Java

  Java utilities for Bioinformatics

• pyfaidx

  1 440 6.0 Python

  Efficient pythonic random access to fasta subsequences

• snippy

  6 437 3.9 Perl

  :scissors: :zap: Rapid haploid variant calling and core genome alignment

• PostGUI

  2 424 0.0 JavaScript

  A React web application to query and share any PostgreSQL database.

• maftools

  3 415 6.6 R

  Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

• hap.py

  2 393 0.0 C++

  Haplotype VCF comparison tools

  

• SaaSHub

  www.saashub.com featured

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Genomics related posts

• Biowasm – Run C/C++ genomics tools in the browser

  1 project | news.ycombinator.com | 11 Mar 2024

• Interactive Examples for Learning Jq

  13 projects | news.ycombinator.com | 7 Nov 2023

• NHI Genome Studies: Mexico Govt Sept 12 Congressional hearing

  4 projects | /r/genetics | 14 Sep 2023

• Invitación a proyecto - Biopython en Español

  1 project | /r/devsarg | 23 Jul 2023

• Snakemake – A framework for reproducible data analysis

  6 projects | news.ycombinator.com | 15 Jul 2023

• All identified polymorphisms in a given gene, how to find?

  2 projects | /r/genetics | 14 Jun 2023

• Biopython – Python Tools for Computational Molecular Biology

  1 project | news.ycombinator.com | 28 May 2023
• A note from our sponsor - SaaSHub
  www.saashub.com | 4 May 2024

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