TAXAassign statistics

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Tool usage distribution map

This map represents all the scientific publications referring to TAXAassign per scientific context

Associated diseases

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Prediction-based taxonomic classification

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TAXAassign specifications

Desktop

Information

Unique identifier	OMICS_21514
Name	TAXAassign
Software type	Application/Script
Interface	Command line interface
Restrictions to use	None
Input data	A nucleotide sequence.
Operating system	Unix/Linux
Programming languages	Perl, Python, Shell (Bash)
Computer skills	Advanced
Version	0.4
Stability	Stable
Requirements	GNU Parallel, Blastn, NCBI's nt database, BioSQL, sqlite3 and MySQL
Maintained	Yes

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Documentation

Issues: https://github.com/umerijaz/taxaassign/issues

TAXAassign citations

(2)

A Large Scale Comparative Metagenomic Study Reveals the Functional Interactions in Six Bloom Forming Microcystis Epibiont Communities

2018

Front Microbiol

PMCID: 5919953

PMID: 29731741

DOI: 10.3389/fmicb.2018.00746

[…] Open reading frames (ORFs) of each genome bin were predicted by Prodigal v2.6.3 in metagenomic mode. We implemented taxonomic assignments of the genome bins using TAXAassign v.0.4 (https://github.com/umerijaz/taxaassign), with some modified codes to improve efficiency and accuracy. Using the improved script, we used deduced amino acid sequence information throu […]

The effect of DNA extraction methodology on gut microbiota research applications

2016

BMC Res Notes

PMCID: 4960752

PMID: 27456340

DOI: 10.1186/s13104-016-2171-7

[…] e then taxonomically classified against the RDP database using the standalone RDPclassifier v2.6 [] with the default–minWords option of 5. For species level assignment, we have used NCBI Taxonomy and TAXAassign (https://github.com/umerijaz/TAXAassign). To find the phylogenetic distances between OTUs, we first multisequence aligned the OTUs against each other using mafft v7.040 [] and then used Fas […]

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