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The Top 23 Python Genomics Sequencing Open Source Projects

Open source projects categorized as Python Genomics Sequencing
Categories > Science > Genomics
Categories > Science > Sequencing
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 4 months ago
Galaxy ⭐ 1,211
Data intensive science for everyone.
dependent packages 23total releases 30most recent commit 3 months agopypi galaxy-util} Downloads
Adam ⭐ 966
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
dependent packages 17total releases 14most 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 104most recent commit 3 months agopypi hgvs} Downloads
Circlator ⭐ 193
A tool to circularize genome assemblies
total releases 33most recent commit 8 months ago
Readfish ⭐ 152
CLI tool for flexible and fast adaptive sampling on ONT sequencers
total releases 9most recent commit 4 months ago
Ariba ⭐ 135
Antimicrobial Resistance Identification By Assembly
dependent packages 1total releases 54most recent commit a year agopypi ariba} Downloads
Gubbins ⭐ 133
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
most recent commit 5 months ago
Xpore ⭐ 122
Identification of differential RNA modifications from nanopore direct RNA sequencing
total releases 20most recent commit 5 months ago
Catch ⭐ 63
A package for designing compact and comprehensive capture probe sets.
most recent commit 6 months ago
Chanjo ⭐ 48
Chanjo provides a better way to analyze coverage data in clinical sequencing.
most recent commit 6 months ago
Fastaq ⭐ 45
Python3 scripts to manipulate FASTA and FASTQ files
dependent packages 7total releases 21most recent commit 2 years agopypi pyfastaq} Downloads
Iva ⭐ 37
de novo virus assembler of Illumina paired reads
total releases 16most recent commit 3 years ago
Biocommons.seqrepo ⭐ 34
non-redundant, compressed, journalled, file-based storage for biological sequences
dependent packages 12total releases 42most recent commit 3 months agopypi biocommons.seqrepo} Downloads
Wochenende ⭐ 30
Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3
most recent commit 2 years ago
Cpipe ⭐ 29
The open source version of the Melbourne Genomics Health Alliance Exome Sequencing Pipeline
most recent commit 6 years ago
Smallrnaseq ⭐ 26
small rna-seq analysis package
total releases 6most recent commit a year ago
Teaching ⭐ 25
This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.
most recent commit 3 months ago
Checkqc ⭐ 23
CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
most recent commit 4 months ago
Gff3toembl ⭐ 20
Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
most recent commit 5 years ago
Ngcgh ⭐ 17
Tools for producing pseudo-cgh of next-generation sequencing data
total releases 14most recent commit 8 years ago
Bioutils ⭐ 16
provides common tools and lookup tables used primarily by the hgvs and uta packages
dependent packages 8total releases 62most recent commit 3 months agopypi bioutils} Downloads
Plasmidtron ⭐ 16
Assembling the cause of phenotypes and genotypes from NGS data
most recent commit 4 years ago
The 7 Most Depended On Python Genomics Sequencing 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
Biocommons.seqrepo ⭐ 34
non-redundant, compressed, journalled, file-based storage for biological sequences
dependent packages 12total releases 42latest release November 13, 2023most recent commit 3 months agopypi biocommons.seqrepo} 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
Bioutils ⭐ 16
provides common tools and lookup tables used primarily by the hgvs and uta packages
dependent packages 8total releases 62latest release July 10, 2023most recent commit 3 months agopypi bioutils} Downloads
Fastaq ⭐ 45
Python3 scripts to manipulate FASTA and FASTQ files
dependent packages 7total releases 21latest release February 19, 2018most recent commit 2 years agopypi pyfastaq} Downloads
Ariba ⭐ 135
Antimicrobial Resistance Identification By Assembly
dependent packages 1total releases 54latest release September 07, 2020most recent commit a year agopypi ariba} Downloads
The 10 Latest Releases In Python Genomics Sequencing 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
Biocommons.seqrepo ⭐ 34
non-redundant, compressed, journalled, file-based storage for biological sequences
dependent packages 12total releases 42latest release November 13, 2023most recent commit 3 months agopypi biocommons.seqrepo} Downloads
Readfish ⭐ 152
CLI tool for flexible and fast adaptive sampling on ONT sequencers
total releases 9latest release October 12, 2023most recent commit 4 months ago
Bioutils ⭐ 16
provides common tools and lookup tables used primarily by the hgvs and uta packages
dependent packages 8total releases 62latest release July 10, 2023most recent commit 3 months agopypi bioutils} 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
Xpore ⭐ 122
Identification of differential RNA modifications from nanopore direct RNA sequencing
total releases 20latest release October 08, 2021most recent commit 5 months ago
Mimsi ⭐ 12
Microsatellite Instability Classification using Multiple Instance Learning
total releases 1latest release March 26, 2021most recent commit 2 years ago
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