============================================================================================= VTAM - Validation and Taxonomic Assignation of Metabarcoding Data

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VTAM is a metabarcoding package with various commands to process high throughput sequencing (HTS) data of amplicons of one or several metabarcoding markers in FASTQ format and produce a table of amplicon sequence variants (ASVs) assigned to taxonomic groups. If you use VTAM in scientific works, please cite the following article:

González, A., Dubut, V., Corse, E., Mekdad, R., Dechatre, T. and Meglécz, E.. VTAM: A robust pipeline for processing metabarcoding data using internal controls. bioRxiv: 10.1101/2020.11.06.371187v1 <https://www.biorxiv.org/content/10.1101/2020.11.06.371187v1>_.

Commands for a quick installation:

.. code-block:: bash

conda create --name vtam python=3.9 -y
conda activate vtam

Then install dependencies

.. code-block:: bash

python3 -m pip install cutadapt
conda install -c bioconda blast -y
conda install -c bioconda vsearch -y
python3 -m pip install vtam

Commands for a quick working example:

.. code-block:: bash

vtam example
cd example
snakemake --printshellcmds --resources db=1 --snakefile snakefile.yml --cores 4 --configfile asper1/user_input/snakeconfig_mfzr.yml --until asvtable_taxa

The table of amplicon sequence variants (ASV) is here:

.. code-block:: bash

(vtam) user@host:~/vtam/example$ head -n4 asper1/run1_mfzr/asvtable_default_taxa.tsv
run marker  variant sequence_length read_count  tpos1_run1  tnegtag_run1    14ben01 14ben02 clusterid   clustersize chimera_borderlineltg_tax_id    ltg_tax_name    ltg_rank    identity    blast_db    phylum  class   order   family  genus   species sequence
run1    MFZR    25  181 478 478 0   0   0   25  1   False   131567  cellular organisms  no rank 80  coi_blast_db_20200420                           ACTATACCTTATCTTCGCAGTATTCTCAGGAATGCTAGGAACTGCTTTTAGTGTTCTTATTCGAATGGAACTAACATCTCCAGGTGTACAATACCTACAGGGAAACCACCAACTTTACAATGTAATCATTACAGCTCACGCATTCCTAATGATCTTTTTCATGGTTATGCCAGGACTTGTT
run1    MFZR    51  181 165 0   0   0   165 51  1   False                   coi_blast_db_20200420       ACTATATTTAATTTTTGCTGCAATTTCTGGTGTAGCAGGAACTACGCTTTCATTGTTTATTAGAGCTACATTAGCGACACCAAATTCTGGTGTTTTAGATTATAATTACCATTTGTATAATGTTATAGTTACGGGTCATGCTTTTTTGATGATCTTTTTTTTAGTAATGCCTGCTTTATTG
run1    MFZR    88  175 640 640 0   0   0   88  1   False   1592914 Caenis pusilla  species 100 coi_blast_db_20200420   Arthropoda  Insecta Ephemeroptera   Caenidae    Caenis  Caenis pusilla  ACTATATTTTATTTTTGGGGCTTGATCCGGAATGCTGGGCACCTCTCTAAGCCTTCTAATTCGTGCCGAGCTGGGGCACCCGGGTTCTTTAATTGGCGACGATCAAATTTACAATGTAATCGTCACAGCCCATGCTTTTATTATGATTTTTTTCATGGTTATGCCTATTATAATC

The database of intermediate data is here:

.. code-block:: bash

(vtam) user@host:~/vtam/example$ sqlite3 asper1/db.sqlite '.tables'

FilterChimera Sample FilterChimeraBorderline SampleInformation FilterCodonStop SortedReadFile FilterIndel TaxAssign FilterLFN Variant FilterLFNreference VariantReadCount FilterMinReplicateNumber wom_Execution FilterMinReplicateNumber2 wom_FileInputOutputInformation FilterMinReplicateNumber3 wom_Option FilterPCRerror wom_TableInputOutputInformation FilterRenkonen wom_TableModificationTime Marker wom_ToolWrapper ReadCountAverageOverReplicates wom_TypeInputOrOutput Run

The VTAM documentation <http://vtam.readthedocs.org/>_ is hosted at ReadTheDocs.

VTAM is maintained by Aitor González (aitor dot gonzalez at univ-amu dot fr) and Emese Meglécz (emese dot meglecz at univ-amu dot fr).