Import the zip archive containing input files from Zenodo db_v05_r117.fasta This reference database has been extracted from the release 117 of EMBL using ecoPCR the file containing the reference database in a fasta format:.the tags correspond to short and specific sequences added on the 5’ end of each primer to distinguish the different samples.the file describing the primers and tags used for all samples sequenced:.FASTQ files resulting from a GA IIx (Illumina) paired-end (2 x 108 bp) sequencing assay of DNA extracted and amplified from four wolf faeces:.The data needed to run the tutorial are the following:
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The OBITools programs imitate Unix standard programs because they usually act as filters. any Galaxy tools corresponding to classical unix command such as less, awk, sort, wc to check your files.obistat to get some basic statistics (count, mean, standard deviation) on the attributes (key=value combinations) in the header of each sequence record (see The extended OBITools fasta format in the fasta format description).
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obihead and obitail to view the first or last sequence records of a file.obicount to count the number of sequence records in a file.Some commands are designed for that purpose, for example you can use :
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It is always a good idea to have a look at the intermediate results or to evaluate the best parameter for each step. 2011), together with a wolf blocking oligonucleotide. After extracting DNA from the faeces, the DNA amplifications were carried out using the primers TTAGATACCCCACTATGC and TAGAACAGGCTCCTCTAG amplifying the 12S-V5 region ( Riaz et al. The data used in this tutorial correspond to the analysis of four wolf scats, using the protocol published in SHEHZAD et al. Based on this OBITools official tutorial, you will learn here how to analyze DNA metabarcoding data produced on Illumina sequencers using: