Top 6 Python Genome Projects

deepvariant

5 3,076 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

DNABERT

1 543 3.1 Python

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!

InfluxDB

www.influxdata.com sponsored

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.
NanoSim

1 213 5.6 Python

Nanopore sequence read simulator
OSGenome

2 107 3.2 Python

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

Project mention: How to get a DNA report using AncestryDNA/23andme raw data without uploading to another server? | /r/bioinformatics | 2023-04-28

I think OSGenome by u/Sweet-Sir-10 would do the trick.

Genome

1 3 2.7 Python

Genome Network Ala Neural Network (by DanShai)
bioinformatics

1 3 6.5 Python

Bioinformatic algorithms for the UCLA Bioinformatics Specialization (by ashinzekene)

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).