Taxy

Taxonomy assignment of ASVs

Getting help

Any issues/requests/problems/comments that are not yet addressed on this page can be posted on Github issues and I will try to reply the same day.

Or you can contact me directly through the following email address:

nicolasdierckxsens at hotmail dot com

Instructions

1. Install dependencies

• Install BLAST

• Install MAFFT

• Install Perl modules: MCE::Child && MCE::Channel

  cpan install MCE

With Conda:

conda create -n taxy -c conda-forge -c bioconda perl

conda install blast

conda install mafft

conda install perl-mce

2. Download local databases

• Nucleotide database - Can be downloaded or updated automatically with the following script:

  https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/blast/update_blastdb.pl

  Instructions: https://www.ncbi.nlm.nih.gov/books/NBK569850/

  perl update_blastdb.pl –decompress nt

• Taxonomy database - Can be downloaded here:

  http://ftp.ebi.ac.uk/pub/databases/ena/taxonomy/taxonomy.xml.gz

3. Run Taxy

perl Taxy0.1.pl -c config.txt

Configuration file

This is an example of a configuration file for the assembly of a chloroplast. To make the assembler work, your configuration file has to have the exact same structure. (Make sure there is always a space after the equals sign and every parameter is captured in one single line)

1. Example of configuration file:

Project name              = Test
Combined reads or ASVs    = /path/to/reads/or/ASVs/ASVs.fasta
Forward reads             = /path/to/reads/reads_1.fastq (at the moment only the ASV option is available)
Reverse reads             = /path/to/reads/reads_2.fastq (at the moment only the ASV option is available)
Keep read ids             = 
Nucleotide database       = /path/to/nucleotide/database/from/NCBI/nt
Taxonomy database         = /path/to/taxanomy/database/from/NCBI/taxonomy.xml
Taxonomy only             = yes
Threads                   = 4
Output path               = /path/to/output/folder/

2. Explanation parameters:

#Project name              = Choose a name for your project, it will be used for the output files.
#Combined reads or ASVs    = /home/nicolas/Perl/OIST/eDNA/Michael/NC_asv_table.fasta
#Forward reads             = The path to the file that contains the forward reads (not necessary when there is a Combined or ASV file)
#Reverse reads             = The path to the file that contains the reverse reads (not necessary when there is a Combined or ASV file)
#Keep read ids             = When yes, the read ids from the fasta or fastq files are used in the output files, otherwise they will be changed to numbers (yes/no)
#Nucleotide database       = /path/to/nucleotide/database/from/NCBI/nt (https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/blast/update_blastdb.pl) (Other databeses with the same structure can also be used)
#Taxonomy database         = /home/nicolas/Perl/OIST/eDNA/taxonomy.xml (http://ftp.ebi.ac.uk/pub/databases/ena/taxonomy/taxonomy.xml.gz)
#Taxonomy only             = When yes, ASVs will directly be used for taxonomy assignment without prior clustering. (yes/no)
#Threads                   = Increasing the number of cores will speed up the runtime.
#Output path               = You can change the directory where all the output files wil be stored.