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Metainformation Template

CV terms

Issue 84 metadata key Corresponding bio.tools CV term Type of value or list of values
Homepage    
Developmental stage of the tool maturity (Emerging, Mature , Legacy)
Topic (could be ELIXIR Community)  
Software or data license license string
Description   multiline varchar (max. 50 lines)
Input format see EBI 1
Tool operation (function) see link 2
Output data see EBI  
Credits and support entity type, entity role  

Modelling and simulation, Optimisation and refinement, Prediction and recognition, Quantification, Service management, Validation, Visualisation


Template

Homepage

Maturity

Topic

License

Description

Input format

Tool operation

Output data

Credits, support

Bioinformatic tools


Disclaimer: Changes in the tool display

We recently created a NFDI4Microbiota domain on the life sciences software registry bio.tools and we will soon be displaying all the tools that NFDI4Microbiota created as well as the ones that NFDI4Microbiota consortium members endorse and highly recommend.

Thank you for your patience while we sort out editing rights and collection labels. Below you can browse tool recommendations from our consortium members.

bakta

Homepage

https://github.com/oschwengers/bakta

maturity

Mature

topic

nnotation of bacterial genomes and plasmids

license

GPL-3.0

Description

Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations in machine-readable JSON & bioinformatics standard file formats for automated downstream analysis.

Input format

(zipped) fasta

Tool operation

annotation

Output data

.tsv: annotations as simple human readble TSV .gff3: annotations & sequences in GFF3 format .gbff: annotations & sequences in (multi) GenBank format .embl: annotations & sequences in (multi) EMBL format .fna: replicon/contig DNA sequences as FASTA .ffn: feature nucleotide sequences as FASTA .faa: CDS/sORF amino acid sequences as FASTA .hypotheticals.tsv: further information on hypothetical protein CDS as simple human readble tab separated values .hypotheticals.faa: hypothetical protein CDS amino acid sequences as FASTA .json: all (internal) annotation & sequence information as JSON .txt: summary as TXT .png: circular genome annotation plot as PNG .svg: circular genome annotation plot as SVG

Credits, support


andi

Homepage

http://github.com/evolbioinf/andi/

maturity

Mature

topic

Phylogenetic analysis

license

GPL-v3

Description

Andi estimates the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.

Input

2 fasta files

Tool operation

Calculation

Output data

txt (distance matrix)

Credits, support


xenoseq

Homepage

https://github.com/bramvandijk88/xenoseq

maturity

Mature

topic

Metagenomics, horizontal gene transfer

license

GPL-3.0

Description

Pipeline to automate the comparison between short-read libraries to detect foreign (“xenotypic”) sequences.

Input format

fastq, tsv

Tool operation

Sequence analysis

Output data

fasta, tsv

Credits, support

  • github: @bramvandijk88

syntenet

Homepage

https://doi.org/doi:10.18129/B9.bioc.syntenet

maturity

Mature

topic

Inference And Analysis Of Synteny Networks

license

GPL-3.0

Description

syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-based phylogeny reconstruction with maximum likelihood.

Input format

fasta, gff, gtf

Tool operation

Phylogenetic Inference

Output data

R data.frame

Credits, support

  • github: @almeidasilvaf
  • doi:10.1093/bioinformatics/btac806

DeLTA2

Homepage

https://gitlab.com/dunloplab/delta

maturity

Mature

topic

Bioimage segmentation and tracking

license

MIT

Description

DeLTA (Deep Learning for Time-lapse Analysis) is a deep learning-based image processing pipeline for segmenting and tracking single cells in time-lapse microscopy movies.

Input format

czi, tiff, png, jpg

Tool operation

Classication

Output data

tiff, tsv

Credits, support

  • gitlab: @jblugagne
  • doi:10.1371/journal.pcbi.1009797

Omnipose

Homepage

https://github.com/kevinjohncutler/omnipose

maturity

Mature

topic

Bioimage segmentation

license

Omnipose NonCommercial License

Description

Omnipose is a general image segmentation tool that builds on Cellpose in a number of ways described in our paper. It works for both 2D and 3D images and on any imaging modality or cell shape, so long as you train it on representative images.

Input format

czi, tiff, png, jpg

Tool operation

Classification

Output data

tiff, hdf5

Credits, support

  • github: @kevinjohncutler
  • doi:10.1038/s41592-022-01639-4

RAREFAN

Homepage

http://rarefan.evolbio.mpg.de

maturity

Mature

topic

Genome sequence analysis

license

MIT

Description

The RAREFAN webserver aims to identify and analyze RAYT transposases and their associated REPIN (Repetitive Extragenic PalINdromic sequences) in bacterial species. The input to the server is a selection of closely related strains (less than 5% divergence). Our service provides an analysis of REPIN population size, how it relates to REPIN replication rate and the presence and absence of RAYTs across all submitted genomes.

Input

fasta

Tool operation

Genome annotation

Output data

gff3, html, R

Credits, support

  • github: @CFGrote
  • doi:10.24072/pcjournal.244

ProteinOrtho

Homepage

https://gitlab.com/paulklemm_PHD/proteinortho

maturity

Mature

topic

Comparative Genomics, Orthology

license

GPL-3.0

Description

Proteinortho is a tool to detect orthologous genes within different species. For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. Input: Multiple fasta files (orange boxes) with many proteins/genes (circles). Output: Groups (.proteinortho) and pairs (.proteinortho-graph) of orthologs proteins/genes. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at one. To enhance the prediction accuracy, the relative order of genes (synteny) can be used as additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF (doi:10.1371/journal.pone.0105015), is already build in Proteinortho.

Input

FASTA

Tool operation

Analysis, Clustering

Output data

tsv, graph, html, xml

Credits, support

  • gitlab: @paulklemm_PHD
  • doi:10.1186/1471-2105-12-124

vConTACT

Homepage

### maturity Mature

topic

Taxonomy

license

GPL-3.0

Description

vConTACT2 is a tool to perform guilt-by-contig-association classification of viral genomic sequence data. It’s designed to cluster and provide taxonomic context of viral metagenomic sequencing data.

Input

FASTA

Tool operation

classification

Output data

TSV, network file, annotation file

Credits, support


VirFinder

Homepage

https://github.com/jessieren/VirFinder

maturity

Mature

topic

Prediction of viral sequences

license

USC-RL v1.0

Description

The package provides functions to predict viral sequences in a fasta file, such as the assembled contigs from metagenomic data. The method has good prediction accuracy for short (~1kb) and noval viral sequences. The prediction method is based on the sequence signatures (k-tuple word frequencies) that distinguish virus from host sequences. The model was trained using equal number of known viral and host sequences. For a query sequence, the number of occurrences of k-tuple words are first counted by a c++ program using a hash table. Then the sequence is predicted based on the k-tuple word frequencies using a logistic regression model trained with previously known sequences.

Input

FASTA

Tool operation

R

Output data

TSV

Credits, support

  • code: https://github.com/jessieren/VirFinder
  • doi:

deepARG

Homepage

https://github.com/gaarangoa/deeparg

Maturity

Mature

Topic

Antibiotic Resistance Genes Prediction from metagenomes

License

MIT The databases used may have commercial restrictions

Description

The deepARG tool leverages deep learning techniques to predict antibiotic resistance genes (ARGs) from genetic sequences. It is designed to handle both DNA and protein sequences, making it versatile for various research applications. By using advanced machine learning algorithms, deepARG can accurately identify and categorize ARGs. Detailed documentation and usage instructions are provided in the GitHub repository, including how to install, run the tool, and interpret its outputs.

Input

  • DNA sequences (fasta)
  • Protein sequences (faa)
  • Short reads (fast)

    Tool Operation

  • Genome annotation

    Output Data

  • tsv
  • Predictions of antibiotic resistance genes with associated metadata

    Credits, Support

  • Creator: Gustavo Arango-Argoty
  • github: @gaarangoa
  • doi: 10.1186/s40168-018-0401-z

Qiita

Homepage

https://qiita.ucsd.edu/

maturity

Mature

topic

Multiomics databasing analysis

license

BSD 3-Clause

Description

Qiita (canonically pronounced cheetah) is an entirely open-source microbial study management platform. It allows users to keep track of multiple studies with multiple ‘omics data. Additionally, Qiita is capable of supporting multiple analytical pipelines through a 3rd-party plugin system, allowing the user to have a single entry point for all of their analyses. Qiita provides database and compute resources to the global community, alleviating the technical burdens that are typically limiting for researchers studying microbial ecology (e.g. familiarity with the command line or access to compute power). Qiita’s platform allows for quick reanalysis of the datasets that have been deposited using the latest analytical technologies. This means that Qiita’s internal datasets are living data that is periodically re-annotated according to current best practices.

Input format

FASTQ, SAM

Tool operation

Analysis, Data handling

Output data

SAM, Tables, visualizations

Credits, support


GTDBTk

Homepage

https://github.com/Ecogenomics/GTDBTk https://ecogenomics.github.io/GTDBTk/

Maturity

Mature and under constant development

Topic

Bacterial and Archaeal Genome Taxonomic classification, Phylogenetic Analysis

License

GPL-3.0

Description

GTDBTk (Genome Taxonomy Database Toolkit) is a software toolkit designed to classify bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB). It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. GTDBTk aims to standardize microbial taxonomy, facilitating consistent and reproducible microbial diversity studies.

Input

  • Genomic sequences (fasta, both complete and draft genomes)

    Tool Operation

  • Taxonomic classification based on the Genome Taxonomy Database
  • Phylogenetic tree construction

    Output Data

  • tsv, fasta, tree

    Credits, Support

  • Chaumeil PA, et al. 2022. GTDB-Tk v2: memory friendly classification with the Genome Taxonomy Database. Bioinformatics, btac672.
  • doi: 10.1093/bioinformatics/btac672

PlasFlow

Homepage

https://github.com/smaegol/PlasFlow

Maturity

Mature

Topic

Plasmid Prediction in Metagenomics contigs

License

GPL-3.0

Description

PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. It relies on the neural network models trained on full genome and plasmid sequences and is able to differentiate between plasmids and chromosomes with accuracy reaching 96%. It outperforms other available solutions for plasmids recovery from metagenomes and incorporates the thresholding which allows for exclusion of incertain predictions. PlasFlow has been published in Nucleic Acids Research (https://doi.org/10.1093/nar/gkx1321).

Input

  • Nucleotide sequences (fasta format)

    Tool Operation

  • Sequence Classification

    Output Data

  • tsv (Classification results indicating plasmid or chromosomal origin)

    Credits, Support

  • Created by S. Maegol
  • Krawczyk PS, Lipinski L, Dziembowski A. Nucleic Acids Res. 2018 Apr 6;46(6):e35.
  • doi: 10.1093/nar/gkx1321

Get Help

If you have any further questions about the management and analysis of your microbial research data, please contact us: helpdesk@nfdi4microbiota.de (by emailing us you agree to the privacy policy - in German on our website: Contact.)

  1. FASTA, SAM, TSV, CSV, XLSX, Image 

  2. Alignment, Analysis, Annotation, Calculation, Classification, Clustering, Comparison, Conversion, Correlation, Data handling, Design, Generation, Indexing, Mapping, 

Citation

National Research Data Infrastructure for Microbiota Research (NFDI4Microbiota). (2024, September 30). Resources. NFDI4Microbiota Knowledge Base.