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PERL program for taxonomic assignment of 16S high-quality reads from RMQS soils using USEARCH program and SILVA database

Authors: TERRAT, Sébastien; DEQUIEDT, Samuel; KARIMI, Battle; CHEMIDLIN PREVOST-BOURE, Nicolas; MARON, Pierre-Alain; RANJARD, Lionel;

PERL program for taxonomic assignment of 16S high-quality reads from RMQS soils using USEARCH program and SILVA database

Abstract

This PERL program was developed to manage easily the taxonomic assignment of 16S high-quality reads using a curated database from SILVA r114 and a dedicated third-party tool called USEARCH. This program takes as input a FASTA file or a folder name containing several FASTA files, another folder name containing the database with specific format (see help for details) and a threshold value defined by the user. Using these three inputs, the program will generate a taxonomic file for high-quality reads using a dedicated approach based on the fiability of taxonomic information from the database from complete reads to environmental reads. More details and information are available when laucnhing the PERL script with the -h option

Keywords

Taxonomy, USEARCH, SILVA, PERL

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selected citations
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This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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