🦠🧬🧑💻📇 Microbial genomes-to-report pipeline
bioinformatics snakemake hpc slurm conda metagenomics bioconda microbial-genomics bacteria clinical-research pbs prokaryotes archaea genomes-to-report apptainer
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- Python
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prokaryotes
Here are 19 public repositories matching this topic...
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
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- Nextflow
UPHL's Reference Free Pipeline
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- Nextflow
We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data. The workflow performs all required pre-processing steps and quality control. Importantly, HRIBO outputs annotation-independent ORF predictions based on two complementary prokaryotic-focused tools, …
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The International Code of Nomenclature of Prokaryotes Described from Sequence Data
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examination of genome size across all kingdoms
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- R
mash works best when given a mash dist file with a bunch of references.
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Command-line tool for retrieving pangenomes using the PanGBank API.
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- Python
A tool for dynamically calculating the codon usage bias in bacterial genomes and querying of a database for Codon Bias statistical analysis
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- Python
panicmage can estimate gene gain and loss rates, the size of pan-genomes, and test for neutral evolution.
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- C++
Software tool designed to accurately identify the genetic translation table (GTT) used in prokaryotic organisms.
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- Python
Modelling evolution of genome size in prokaryotes in response to changes in their abiotic environment
genome cpp simulation biology evolution modelling bacteria evolution-simulation genome-size prokaryotes genome-size-evolution
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- Python
Sup. Table 1 from Rodríguez-Gijón and Nuy et al., 2022 (Front. in Microbiology)
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Pipeline for improving the Lotus japonicus genomes using an hybrid assembly approach
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- Python
Sequence processing and analysis code used to investigate the effects of different DNA extraction methods and PCR variability on multi-taxon DNA meta-barcoding estimates of soil biodiversity.
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- R
Python CLI tool & package. An LLM-guided Post-Annotation Synthesizer that turns complex prokaryotic genome annotations into human-readable summaries & machine-readable JSON.
python cli json bioinformatics pipeline genomics lms data-analysis genome-annotation prokaryotes prokaryotic-genomes bakta
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Repository hosting code and manuscript materials for DISA project at IITD
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- Java
Variant Calling with Deep Learning for Prokaryotic genomes using TensorFlow. Adds (0 <= P(Variant) <= 1) to VCF files under INFO as abbreviated "ACC=".
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- Jupyter Notebook
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