Metadata-Version: 1.1
Name: vtam
Version: 0.1.20
Summary: VTAM - Validation and Taxonomic Assignation of Metabarcoding Data is a metabarcoding pipeline. The analyses start from high throughput sequencing (HTS) data of amplicons of one or several metabarcoding markers and produce an amplicon sequence variant (ASV) table of validated variants assigned to taxonomic groups.
Home-page: https://vtam.readthedocs.io
Author: Aitor Gonzalez, Thomas Dechatre, Reda Mekdad, Emese Meglecz
Author-email: aitor.gonzalez@univ-amu.fr
License: MIT
Description: =============================================================================================
        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., Dechartre, T., Spinelli, L. and  Meglécz, E.**.
        `VTAM: A robust pipeline for processing metabarcoding data using internal controls`.
        Submitted to **Methods in Ecology and Evolution**.
        
        Commands for a quick installation:
        
        .. code-block:: bash
        
            conda create --name vtam python=3.7 -y
            python3 -m pip install --upgrade cutadapt
            conda install -c bioconda blast
            conda install -c bioconda vsearch
            python3 -m pip install --upgrade 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
        
        Documentation
        -------------
        
        The `VTAM documentation <http://vtam.readthedocs.org/>`_ is hosted at ReadTheDocs.
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: Microsoft :: Windows :: Windows 10
