Genome

Open-source projects categorized as Genome
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Language: + Python + Nim + C++ + M4 + Nextflow + Cython + Perl + Haskell + Jupyter Notebook
Topics: Bioinformatics Machine Learning sequencing Annotation Python
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Top 14 Genome Open-Source Projects

  • deepvariant

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

  • mosdepth

    fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

    • Project mention: Calculating Average Coverage or Read Depth for a Sequence (WES) | /r/bioinformatics | 2023-06-24

  • InfluxDB

    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.

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  • DNABERT

    DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

    • Project mention: [D] New to DNABERT | /r/MachineLearning | 2023-11-03

    If I want to get started, they said it's optional to pre-train (so you can skip to step 3). This is where I got tripped up: "Note that the sequences are in kmer format, so you will need to convert your sequences into that." From what I understand, you need to do this so that all of the sequences are the same length? So kmer=6 means all of the sequences are length 6? Someone suggested that I take the first nucleotide in the promoter and grab 3 nucleotides before and 3 nucleotides after (+/-3 bases). I don't think that's how the kmer thing works though? I tried replicating how I think it works down below (I got confused on the last row of the 'after' df). Please correct me if I'm wrong!

  • Augustus

    Genome annotation with AUGUSTUS (by Gaius-Augustus)

  • masurca

  • NanoSim

    Nanopore sequence read simulator

  • eager

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline

  • SaaSHub

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  • pyrodigal

    Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

    • Project mention: DNA to amino acid sequence? | /r/bioinformatics | 2023-06-19

    True! I believe bakta relies on this python implementation of prodigal for translation https://github.com/althonos/pyrodigal

  • OSGenome

    An Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies

  • PGA

    Plastid Genome Annotator

  • hmep

    Haskell Multi Expression Programming implemented with the focus on speed

  • bioinformatics

    Bioinformatic algorithms for the UCLA Bioinformatics Specialization (by ashinzekene)

  • Genome

    Genome Network Ala Neural Network (by DanShai)

  • DIF

    "DNA IMAGE FOOTPRINT" The main idea is to convert a DNA sequence to an image to find any related sequences in the image with common algorithms (by MahdiKarimian)

  • SaaSHub

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NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).

Genome related posts

Index

What are some of the best open-source Genome projects? This list will help you:

Project Stars
1 deepvariant 3,080
2 mosdepth 656
3 DNABERT 543
4 Augustus 264
5 masurca 229
6 NanoSim 213
7 eager 124
8 pyrodigal 122
9 OSGenome 107
10 PGA 46
11 hmep 7
12 bioinformatics 3
13 Genome 3
14 DIF 1

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