UPIMAPI
atlas
UPIMAPI | atlas | |
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3 | 2 | |
26 | 349 | |
- | 2.0% | |
7.5 | 8.9 | |
5 months ago | 22 days ago | |
Python | Python | |
BSD 3-clause "New" or "Revised" License | BSD 3-clause "New" or "Revised" License |
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UPIMAPI
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Any programs/packages that will allow me to compare cluster annotations obtained from metagenomic data?
You may run MOSCA (https://github.com/iquasere/MOSCA), it performs all major steps of metagenomics analysis. It includes that functional classification you are looking for, since with UPIMAPI (https://github.com/iquasere/UPIMAPI) it annotates with UniProt DB as reference, and obtains information including taxonomy, EC numbers, and even those GOs, and reCOGnizer (https://github.com/iquasere/reCOGnizer), which annotates with CDD DB as reference, and obtains orthologous groups information (COG, Pfam, etc).
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Metatranscriptomics Workflow Questions?
Prediction of coding sequences takes as input the contigs you obtained, and gives you the translated genes. Besides annotating with the KEGG database, you may also want to annotate with more general purpose databases (e.g. UniProt), as these provide more taxonomies and functional information. MOSCA includes UPIMAPI (https://github.com/iquasere/UPIMAPI) and reCOGnizer (https://github.com/iquasere/reCOGnizer), which annotate genes with reference to UniProt and CDD databases using two different methods, providing complementary information. This is the same methodology used by widely popular tools such as eggNOG-mapper and Prokka, but these use other databases.
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Problems using Prokka
Install with mamba instead of conda, no more problems. Or use UPIMAPI (https://github.com/iquasere/UPIMAPI) together with reCOGnizer (https://github.com/iquasere/reCOGnizer), since these tools obtain better results when annotating proteins
atlas
- Resources to learn genetic data manipulation basics?
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Is it possible to calculate relative abundance of microorganisms in a community through shotgun-metagenomics?
You might want to check Atlas, an assembly/binning based pipeline for metagenomics data Publication Github
What are some alternatives?
ncbi-genome-download - Scripts to download genomes from the NCBI FTP servers
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
pypsa-eur - PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System
GraphBin2 - ☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
zarp - The Zavolab Automated RNA-seq Pipeline
chipseq-smk-pipeline - ChIP-Seq processing pipeline on snakemake
eggnog-mapper - Fast genome-wide functional annotation through orthology assignment
bioinformatics - :microscope: Path to a free self-taught education in Bioinformatics!
biopython-coronavirus - Biopython Jupyter Notebook tutorial to characterize a small genome