vtam 0.2.0
VTAM - Validation and Taxonomic Assignation of Metabarcoding Data is a metabarcoding pipeline. The analysis starts from high throughput sequencing (HTS) data of amplicons of one or several metabarcoding markers and produces an amplicon sequence variant (ASV) table of validated variants assigned to taxonomic groups.
License: MIT

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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).