reCOGnizer
A tool for domain based annotation with databases from the Conserved Domains Database (by iquasere)
MOSCA
Meta-Omics Software for Community Analysis (by iquasere)
reCOGnizer | MOSCA | |
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9 | 12 | |
26 | 32 | |
- | - | |
7.4 | 8.2 | |
4 months ago | 3 months ago | |
HTML | Python | |
BSD 3-clause "New" or "Revised" License | GNU General Public License v3.0 only |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
reCOGnizer
Posts with mentions or reviews of reCOGnizer.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-06-01.
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Is there a way to achieve a similar COG annotation for Haloferax mediterranei?
reCOGnizer (https://github.com/iquasere/reCOGnizer) will do that for you. It also outputs the COG categories in a krona plot
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Why do some HMMs come with a separate score table instead of embedding in as cut_ga, cut_tc, or cut_nc?
What tool are you using for analyzing them? Using something like reCOGnizer (https://github.com/iquasere/reCOGnizer) gives you the bitscores and evalues in a TSV table, next to the matches
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Metadbgwas, my tool ! What could I do better ?
Finally, a huge help on developing is having a Continuous Integration/Deployment on the tool. CD refers to the conda suggestion above, as your tool would be readily available in a controlled environment. CI could use the GitHub Actions functionality provided by GitHub. You can see an example here
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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
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How would you name the program that does cog annotation?
I think reCOGnizer is a nice name
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Is there any other tool for COG annotation of the bacterial genome than EggNOG mapper?
reCOGnizer (https://github.com/iquasere/reCOGnizer) can annotate with COGs, and the other databases available at CDD. It obtains all information concerning COGs description and categories, and outputs krona plots and TSV tables in formats easy to analyze. There is also mantis (https://github.com/PedroMTQ/mantis), prokka (https://github.com/tseemann/prokka) and DFAST (https://github.com/nigyta/dfast_core), the latter two work on contigs and the first two are for proteins
MOSCA
Posts with mentions or reviews of MOSCA.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-05-26.
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What is the best software to use for partial or full data analysis on RNA-Seq. The output I will receive is a FASTQ file.
MOSCA (https://github.com/iquasere/MOSCA) performs all major steps of RNA-Seq analysis in a fully automated workflow, meaning you only have to input your data and it will take care of the rest for you!
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Resources for omics analysis?
MOSCA (https://github.com/iquasere/MOSCA) performs integrated analysis of all of those
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Stuck with RNA seq for ages - please help!!
I developed a script for this type of analysis, it takes as input a count matrix and the underlying conditions (replicates) information, hope it helps
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How to estimate gene transcription levels from metatranscriptomics?
I have developed MOSCA (https://github.com/iquasere/MOSCA) which performs exactly this type of analysis. You can read more about it in the Wiki (https://github.com/iquasere/MOSCA/wiki)
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How to determine gene copies on a metagenome ?
You probably should use some pipeline such as MOSCA (https://github.com/iquasere/MOSCA) and then check on the annotations provided to see which genes contain the same names/functions
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RNA Seq analysis for R
Perhaps this script may help you? https://github.com/iquasere/MOSCA/blob/master/workflow/scripts/de_analysis.R
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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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Qurstion about automating trimming process
I also developed a neet preprocessing script, which uses FastQC reports to inform Trimmomatic on what parameters it should use, seems like exactly what you want. Its use is detailed in MOSCA's wiki, and you can obtain the script directly from GitHub here.
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Metatranscriptomics Workflow Questions?
With MOSCA, would I essentially be following all of the steps here for each of my samples? https://github.com/iquasere/MOSCA/wiki/Partial-runs I have some metagenomes that my lab previously obtained from the same site, but am unsure how I'd integrate them here.
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Expression analysis without conditions
I was recently given six RNA-Seq datasets to identify significantly expressed genes in a specific condition - butyrate degradation in the presence of activated carbon. I already did the major steps of metatranscriptomics analysis using MOSCA (https://github.com/iquasere/MOSCA), and was now wondering how can I determine which proteins have an interesting level of expression.
What are some alternatives?
When comparing reCOGnizer and MOSCA you can also consider the following projects:
Ory Keto - Open Source (Go) implementation of "Zanzibar: Google's Consistent, Global Authorization System". Ships gRPC, REST APIs, newSQL, and an easy and granular permission language. Supports ACL, RBAC, and other access models.
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
prokka - :zap: :aquarius: Rapid prokaryotic genome annotation
orfipy - Fast and flexible ORF finder
guardian_db - Guardian DB integration for tracking tokens and ensuring logout cannot be replayed.
pyfaidx - Efficient pythonic random access to fasta subsequences
progen - Official release of the ProGen models