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The Top 23 Python Ngs Open Source Projects

Open source projects categorized as Python Ngs
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
Galaxy ⭐ 1,211
Data intensive science for everyone.
dependent packages 23total releases 30most recent commit 3 months agopypi galaxy-util} Downloads
Deeptools ⭐ 644
Tools to process and analyze deep sequencing data.
most recent commit a month ago
Snakepipes ⭐ 359
Customizable workflows based on snakemake and python for the analysis of NGS data
most recent commit 3 months ago
Bioconvert ⭐ 344
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
total releases 34most recent commit 5 months ago
Python Musicbrainzngs ⭐ 222
Python bindings for Musicbrainz' NGS webservice
dependent packages 1total releases 1most recent commit 2 years ago
Sortmerna ⭐ 220
SortMeRNA: next-generation sequence filtering and alignment tool
most recent commit 2 months ago
Afterqc ⭐ 157
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
most recent commit 6 years ago
Seq2science ⭐ 132
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
most recent commit 6 months ago
Viral Ngs ⭐ 129
Viral genomics analysis pipelines
most recent commit 4 years ago
Atropos ⭐ 116
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
most recent commit 5 months ago
Crispresso ⭐ 110
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
dependent packages 1total releases 51most recent commit 5 years agopypi CRISPResso} Downloads
Ngscheckmate ⭐ 106
Software program for checking sample matching for NGS data
most recent commit 9 months ago
Cloops ⭐ 99
Accurate and flexible loops calling tool for 3D genomic data.
most recent commit 2 years ago
Isoquant ⭐ 98
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
most recent commit 4 months ago
Reg Gen ⭐ 96
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
most recent commit 7 months ago
Platon ⭐ 93
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
total releases 10most recent commit 8 months ago
Tadbit ⭐ 89
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
most recent commit a year ago
Ngs Pipe ⭐ 87
NGS-pipe: next-generation sequencing pipelines for precision oncology
most recent commit 5 years ago
Bamnostic ⭐ 84
a pure Python multi-version tolerant, runtime and OS-agnostic Binary Alignment Map (BAM) file parser and random access tool
dependent packages 2total releases 56most recent commit a year agopypi bamnostic} Downloads
Recentrifuge ⭐ 83
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
total releases 77most recent commit 4 months ago
Mcclintock ⭐ 83
Meta-pipeline to identify transposable element insertions using next generation sequencing data
most recent commit 4 months ago
Tbprofiler ⭐ 81
Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
most recent commit 4 months ago
The 5 Most Depended On Python Ngs Open Source Projects
Galaxy ⭐ 1,211
Data intensive science for everyone.
dependent packages 23total releases 30latest release December 08, 2023most recent commit 3 months agopypi galaxy-util} Downloads
Oxbow ⭐ 32
Read specialized NGS formats as data frames in R, Python, and more.
dependent packages 2total releases 3latest release October 26, 2023most recent commit 5 months agopypi oxbow} Downloads
Bamnostic ⭐ 84
a pure Python multi-version tolerant, runtime and OS-agnostic Binary Alignment Map (BAM) file parser and random access tool
dependent packages 2total releases 56latest release April 26, 2023most recent commit a year agopypi bamnostic} Downloads
Python Musicbrainzngs ⭐ 222
Python bindings for Musicbrainz' NGS webservice
dependent packages 1total releases 1latest release January 12, 2022most recent commit 2 years ago
Crispresso ⭐ 110
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
dependent packages 1total releases 51latest release June 30, 2018most recent commit 5 years agopypi CRISPResso} Downloads
The 10 Latest Releases In Python Ngs Open Source Projects
Galaxy ⭐ 1,211
Data intensive science for everyone.
dependent packages 23total releases 30latest release December 08, 2023most recent commit 3 months agopypi galaxy-util} Downloads
Monsda ⭐ 10
MONSDA, Modular Organizer of Nextflow and Snakemake driven hts Data Analysis
total releases 14latest release November 26, 2023most recent commit 5 months ago
Oxbow ⭐ 32
Read specialized NGS formats as data frames in R, Python, and more.
dependent packages 2total releases 3latest release October 26, 2023most recent commit 5 months agopypi oxbow} Downloads
Microhapdb ⭐ 7
Portable database of microhaplotype marker and allele frequency data
total releases 13latest release October 26, 2023most recent commit 6 months ago
Platon ⭐ 93
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
total releases 10latest release August 10, 2023most recent commit 8 months ago
Bamnostic ⭐ 84
a pure Python multi-version tolerant, runtime and OS-agnostic Binary Alignment Map (BAM) file parser and random access tool
dependent packages 2total releases 56latest release April 26, 2023most recent commit a year agopypi bamnostic} Downloads
Recentrifuge ⭐ 83
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
total releases 77latest release January 16, 2023most recent commit 4 months ago
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