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The Top 23 Python Bioinformatics Genome Open Source Projects

Open source projects categorized as Python Bioinformatics Genome
Categories > Data Processing > Bioinformatics
Categories > Science > Genome
Deepvariant ⭐ 2,978
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
Hail ⭐ 905
Cloud-native genomic dataframes and batch computing
dependent packages 17total releases 146most recent commit 3 months agopypi hail} Downloads
Ncbi Genome Download ⭐ 784
Scripts to download genomes from the NCBI FTP servers
dependent packages 6total releases 25most recent commit 9 months agopypi ncbi-genome-download} Downloads
Jcvi ⭐ 650
Python library to facilitate genome assembly, annotation, and comparative genomics
dependent packages 1total releases 97most recent commit 4 months agopypi jcvi} Downloads
Sniffles ⭐ 479
Structural variation caller using third generation sequencing
total releases 8most recent commit 3 months 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 agopypi gtdbtk} Downloads
Bakta ⭐ 365
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
total releases 37most recent commit 3 months ago
Genometools ⭐ 261
GenomeTools genome analysis system.
most recent commit 6 months ago
Pygeno ⭐ 242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
total releases 18most recent commit 4 years ago
Hgvs ⭐ 226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 12total releases 104most recent commit 3 months agopypi hgvs} Downloads
Pyfastx ⭐ 211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dependent packages 20total releases 68most recent commit 5 months agopypi pyfastx} Downloads
Drep ⭐ 199
Rapid comparison and dereplication of genomes
dependent packages 1total releases 63most recent commit 7 months agopypi drep} Downloads
Circlator ⭐ 193
A tool to circularize genome assemblies
total releases 33most recent commit 8 months ago
Ppanggolin ⭐ 191
Build a partitioned pangenome graph from microbial genomes
total releases 6most recent commit 3 months ago
Insilicoseq ⭐ 158
🚀 A sequencing simulator
dependent packages 1total releases 37most recent commit 4 months agopypi InSilicoSeq} Downloads
Metagem ⭐ 155
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
most recent commit 4 months ago
Pyani ⭐ 140
Application and Python module for average nucleotide identity analyses of microbes.
dependent packages 1total releases 18most recent commit 2 years agopypi pyani} Downloads
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 50most recent commit 5 months agopypi SigProfilerExtractor} Downloads
Toga ⭐ 120
TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.
most 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 60most recent commit 3 months agopypi pyrodigal} Downloads
Instrain ⭐ 104
Bioinformatics program inStrain
total releases 59most recent commit 8 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 102most recent commit 3 months agopypi SigProfilerMatrixGenerator} Downloads
Bioinformatics ⭐ 90
Code inspired by Bioinformatics Algorithms: an Active Learning Approach.
most recent commit a year ago
The 10 Most Depended On Python Bioinformatics Genome Open Source Projects
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 agopypi pyfastx} Downloads
Hail ⭐ 905
Cloud-native genomic dataframes and batch computing
dependent packages 17total releases 146latest release October 30, 2023most recent commit 3 months agopypi hail} Downloads
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 agopypi pyrodigal} Downloads
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 agopypi hgvs} Downloads
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 agopypi ncbi-genome-download} Downloads
Jcvi ⭐ 650
Python library to facilitate genome assembly, annotation, and comparative genomics
dependent packages 1total releases 97latest release August 30, 2023most recent commit 4 months agopypi jcvi} Downloads
Insilicoseq ⭐ 158
:rocket: A sequencing simulator
dependent packages 1total releases 37latest release August 10, 2023most recent commit 4 months agopypi InSilicoSeq} Downloads
Pyani ⭐ 140
Application and Python module for average nucleotide identity analyses of microbes.
dependent packages 1total releases 18latest release July 27, 2022most recent commit 2 years agopypi pyani} Downloads
The 10 Latest Releases In Python Bioinformatics 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 agopypi pyrodigal} Downloads
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 agopypi pyfastx} Downloads
Genet ⭐ 8
Python library for genome editing and CRISPR research
total releases 37latest release November 24, 2023most recent commit 3 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
Hail ⭐ 905
Cloud-native genomic dataframes and batch computing
dependent packages 17total releases 146latest release October 30, 2023most recent commit 3 months agopypi hail} Downloads
Codonu ⭐ 13
A python project for analysis of codon usage for gene or genome analysis
total releases 8latest release October 01, 2023most recent commit 6 months ago
Drep ⭐ 199
Rapid comparison and dereplication of genomes
dependent packages 1total releases 63latest release September 15, 2023most recent commit 7 months agopypi drep} Downloads
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