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The Top 23 Bacteria Open Source Projects

Open source projects categorized as Bacteria
Categories > Bacteria
Gtdbtk ⭐ 440
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
dependent packages 1total releases 48most recent commit 2 months agopypi gtdbtk} Downloads
Snippy ⭐ 408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
most recent commit 9 months ago
Bakta ⭐ 365
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
total releases 37most recent commit 5 months ago
Ppanggolin ⭐ 191
Build a partitioned pangenome graph from microbial genomes
total releases 6most recent commit 5 months ago
Chewbbaca ⭐ 113
BSR-Based Allele Calling Algorithm
total releases 40most recent commit 5 months ago
Get_homologues ⭐ 98
GET_HOMOLOGUES: a versatile software package for pan-genome analysis
most recent commit 6 months ago
Platon ⭐ 93
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
total releases 10most recent commit 9 months ago
Pyseer ⭐ 81
SEER, reimplemented in python 🐍🔮
total releases 18most recent commit 8 months ago
Nullarbor ⭐ 80
💾 📃 "Reads to report" for public health and clinical microbiology
most recent commit 4 years ago
Pioreactor ⭐ 75
Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.
total releases 27most recent commit 5 months ago
Pangraph ⭐ 72
A bioinformatic toolkit to align genome assemblies into pangenome graphs
most recent commit 6 months ago
Poppunk ⭐ 71
PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
total releases 22most recent commit 7 months ago
Scoary ⭐ 71
Pan-genome wide association studies
total releases 16most recent commit 7 years ago
Bigsdb ⭐ 53
Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
most recent commit 5 months ago
Asap ⭐ 46
A scalable bacterial genome assembly, annotation and analysis pipeline
most recent commit 2 years ago
Bactmap ⭐ 45
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
most recent commit 9 months ago
Seer ⭐ 35
sequence element (kmer) enrichment analysis
most recent commit 2 years ago
Prophyle ⭐ 30
Accurate, resource-frugal and deterministic DNA sequence classifier.
total releases 53most recent commit 7 months ago
Plsdb ⭐ 29
PLSDB pipeline to collect bacterial plasmids from NCBI
most recent commit 8 months ago
Vigen ⭐ 24
viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data
most recent commit a year ago
Socru ⭐ 23
Order and orientation of complete bacterial genomes
most recent commit 6 months ago
Pathogentrack ⭐ 22
A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.
most recent commit 10 months ago
Protozoa ⭐ 21
A simulation of protozoan behavior and evolution
most recent commit a year ago
The 10 Latest Releases In Bacteria Open Source Projects
Pioreactor ⭐ 75
Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.
total releases 27latest release November 29, 2023most recent commit 5 months ago
Bakta ⭐ 365
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
total releases 37latest release November 29, 2023most recent commit 5 months ago
Chewbbaca ⭐ 113
BSR-Based Allele Calling Algorithm
total releases 40latest release November 03, 2023most recent commit 5 months ago
Tadrep ⭐ 18
Targeted Detection and Reconstruction of Plasmids
total releases 3latest release August 21, 2023most recent commit 10 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 9 months ago
Gtdbtk ⭐ 440
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
dependent packages 1total releases 48latest release July 11, 2022most recent commit 2 months agopypi gtdbtk} Downloads
Prophyle ⭐ 30
Accurate, resource-frugal and deterministic DNA sequence classifier.
total releases 53latest release August 23, 2021most recent commit 7 months ago
Poppunk ⭐ 71
PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
total releases 22latest release December 31, 2020most recent commit 7 months ago
Pyseer ⭐ 81
SEER, reimplemented in python 🐍🔮
total releases 18latest release March 22, 2020most recent commit 8 months ago
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