The Top 23 Python Genome Open Source Projects

Open source projects categorized as Python Genome

Categories > Programming Languages > Python

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

most recent commit 5 months ago

Ncov ⭐ 1,348

Nextstrain build for novel coronavirus SARS-CoV-2

most recent commit 3 months ago

Hail ⭐ 905

Cloud-native genomic dataframes and batch computing

dependent packages 17total releases 146most recent commit 3 months ago

Ncbi Genome Download ⭐ 784

Scripts to download genomes from the NCBI FTP servers

dependent packages 6total releases 25most recent commit 9 months ago

Pygenometracks ⭐ 654

python module to plot beautiful and highly customizable genome browser tracks

most recent commit 9 months ago

Jcvi ⭐ 650

Python library to facilitate genome assembly, annotation, and comparative genomics

dependent packages 1total releases 97most recent commit 4 months ago

Ban Vqa ⭐ 527

Bilinear attention networks for visual question answering

most recent commit 6 months ago

Sniffles ⭐ 479

Structural variation caller using third generation sequencing

total releases 8most recent commit 3 months ago

Dnabert ⭐ 471

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

most recent commit 6 months ago

Samplot ⭐ 458

Plot structural variant signals from many BAMs and CRAMs

total releases 3most recent commit 5 months ago

Pytorch Neat ⭐ 387

most recent commit 4 years ago

Gtdbtk ⭐ 383

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

dependent packages 1total releases 48most recent commit 5 months ago

Bakta ⭐ 365

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

total releases 37most recent commit 3 months ago

Snakepipes ⭐ 359

Customizable workflows based on snakemake and python for the analysis of NGS data

most recent commit 3 months ago

Genomepy ⭐ 355

genes and genomes at your fingertips

dependent packages 5total releases 36most recent commit 10 months ago

Liftoff ⭐ 335

An accurate GFF3/GTF lift over pipeline

most recent commit 9 months ago

Na12878 ⭐ 321

Data and analysis for NA12878 genome on nanopore

most recent commit 2 years ago

Atac Seq Pipeline ⭐ 290

ENCODE ATAC-seq pipeline

most recent commit a year ago

Ragtag ⭐ 286

Tools for fast and flexible genome assembly scaffolding and improvement

total releases 7most recent commit a year ago

Rgi ⭐ 283

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

most recent commit 4 months ago

Pycircos ⭐ 277

python Circos

dependent packages 2total releases 3most recent commit 5 months ago

Gemini ⭐ 272

a lightweight db framework for exploring genetic variation.

most recent commit 4 years ago

Trycycler ⭐ 264

A tool for generating consensus long-read assemblies for bacterial genomes

most recent commit 6 months ago

The 10 Most Depended On Python Genome Open Source Projects

Bx Python ⭐ 138

Tools for manipulating biological data, particularly multiple sequence alignments

dependent packages 24total releases 20latest release July 26, 2023most recent commit 4 months ago

Pyfastx ⭐ 211

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

dependent packages 20total releases 68latest release November 25, 2023most recent commit 5 months ago

Hail ⭐ 905

Cloud-native genomic dataframes and batch computing

dependent packages 17total releases 146latest release October 30, 2023most recent commit 3 months ago

Pyliftover ⭐ 47

Pure-python implementation of UCSC liftOver genome coordinate conversion

dependent packages 15total releases 4latest release May 25, 2019most recent commit 5 years ago

Pyrodigal ⭐ 111

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

dependent packages 14total releases 60latest release November 27, 2023most recent commit 3 months ago

Hgvs ⭐ 226

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

dependent packages 12total releases 104latest release November 21, 2022most recent commit 3 months ago

Sigprofilermatrixgenerator ⭐ 91

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

dependent packages 10total releases 102latest release October 02, 2023most recent commit 3 months ago

pypi SigProfilerMatrixGenerator} Downloads

Liftover ⭐ 51

liftover for python, made fast with cython

dependent packages 8total releases 20latest release November 02, 2023most recent commit 6 months ago

Twobitreader ⭐ 12

A fast python class for reading 2-bit files (used by UCSC genome browser)

dependent packages 7total releases 26latest release May 21, 2019most recent commit 3 years ago

Ncbi Genome Download ⭐ 784

Scripts to download genomes from the NCBI FTP servers

dependent packages 6total releases 25latest release July 28, 2023most recent commit 9 months ago

The 10 Latest Releases In Python Genome Open Source Projects

Bakta ⭐ 365

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

total releases 37latest release November 29, 2023most recent commit 3 months ago

Pyrodigal ⭐ 111

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

dependent packages 14total releases 60latest release November 27, 2023most recent commit 3 months ago

Pyfastx ⭐ 211

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

dependent packages 20total releases 68latest release November 25, 2023most recent commit 5 months ago

Genet ⭐ 8

Python library for genome editing and CRISPR research

total releases 37latest release November 24, 2023most recent commit 3 months ago

Gunc ⭐ 49

Python package for detection of chimerism and contamination in prokaryotic genomes.

total releases 8latest release November 23, 2023most recent commit 5 months ago

Pybio ⭐ 7

pybio is a comprehensive Python framework designed to streamline genomics operations. It offers a direct interface to Ensembl genome assemblies and annotations, while also accommodating custom genomes via FASTA/GTF inputs.

dependent packages 2total releases 27latest release November 23, 2023most recent commit 4 months ago

Sigprofilerextractor ⭐ 132

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

dependent packages 3total releases 50latest release November 21, 2023most recent commit 5 months ago

Carveme ⭐ 117

CarveMe: genome-scale metabolic model reconstruction

dependent packages 2total releases 16latest release November 08, 2023most recent commit 4 months ago

Teloclip ⭐ 26

A tool for the recovery of unassembled telomeres from soft-clipped read alignments.

total releases 3latest release November 06, 2023most recent commit 3 months ago

Storf Reporter ⭐ 15

Package to extract Unannotated Regions from prokaryotic genomes report coding and pseudogenised genes delimited by stop codons - Named StORFs (Stop - Open Reading Frames)

total releases 33latest release November 04, 2023most recent commit 3 months ago

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