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Prediction-based taxonomic classification

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TAXAassign specifications

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

TAXAassign in publications

(2)

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

PMCID: 5919953

PMID: 29731741

DOI: 10.3389/fmicb.2018.00746

[…] estimates for each genome bin., 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 […]

The effect of DNA extraction methodology on gut microbiota research applications

PMCID: 4960752

PMID: 27456340

DOI: 10.1186/s13104-016-2171-7

[…] 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 […]

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