# MAGnet
Copying usage parameters from MAGnet repo/README.md/Getting started

```
usage: magnet.py [-h] -c CLASSIFICATION -i FASTQ [-I FASTQ2] [-m {ont,illumina}] -o OUTPUT [-t TAXID_IDX]
                 [-a ABUNDANCE_IDX] [--min-abundance MIN_ABUNDANCE] [--min-mapq MIN_MAPQ]
                 [--min-covscore MIN_COVSCORE] [--threads THREADS] [--include-mag] [--subspecies]

Universal Taxonomic Classification Verifier.

optional arguments:
  -h, --help            show this help message and exit
  -c CLASSIFICATION, --classification CLASSIFICATION
                        Path to the Taxonomic Classification Report. Accepting csv/tsv file format, other text formats
                        are treated as tsv.
  -i FASTQ, --fastq FASTQ
                        Path to the first fastq file.
  -I FASTQ2, --fastq2 FASTQ2
                        Path to the second fastq file for paired-end reads.
  -m {ont,illumina}, --mode {ont,illumina}
                        Modes for different sequencing platforms [ont, illumina]. Default:[ont]
  -o OUTPUT, --output OUTPUT
                        Path to the output directory.
  -t TAXID_IDX, --taxid-idx TAXID_IDX
                        The column index (0-based) of the taxids. Default:[0]
  -a ABUNDANCE_IDX, --abundance-idx ABUNDANCE_IDX
                        The column index (0-based) of the abundance. Default:[None]
  --min-abundance MIN_ABUNDANCE
                        Minimum abundance (0-1) for pre-filtering, exclude taxa below the threshold.
  --min-mapq MIN_MAPQ   Minimum MAPQ for primary alignments. Default:[20]
  --min-covscore MIN_COVSCORE
                        Minimum Coverage Score for supplementary alignments. Default:[0.7]
  --threads THREADS     Number of threads for Multi-threading. Default:[1]
  --include-mag         Include metagenomic assemble genomes. Default:[False]
  --subspecies          Verify taxonomic classification at subspecies rank. Default:[False]
```

Minimal usage:
```
magnet.py -c {lemur_report_file} -i {input_fastq_file} -o {output_path} -m ont
```
