SRA-Importer 0.0.7

An easy and convenient way to import data from the sra database and creating OTU and Taxonomy tables.

SRA-Importer

An easy and convenient way to import data from the sra database and creating OTU and Taxonomy tables.

Importing is divided to 2 stages:

Create Visualization

The first stage is in charge of taking the data from the sra database and make a visualization of the reads. The visualization purpose is to make better assessment of the range in which one should trim and truncate the reads generated by qiime2.

Parameters

• --sra-study: SRA experiment code.
• --acc-list: Accession list file. This file must be stored locally.
• --output-vis-path: An output path for the visualisation. (Optional)

Note: Only one of the following must be given --sra-study/--acc-list. If both are given, an error will be raised.
Usage:

create_visualization --sra-study <sra-study-code> --acc-list <accession-list-file-path> --output-vis-path <final-output-path-of-visualisation>

Export Data

The second stage is in charge of creating OTU and Taxonomy tables and export them into a usable file formats.

Parameters

• --output-dir: The path of the directory created by the first stage.
• --otu-output-file: An output path for the OTU table. The directory must exist, and the file's format must be txt/tsv.
• --taxonomy-output-file: An output path for the taxonomy table. The directory must exist, and the file's format must be tsv.

DADA2 parameters

• --trim: a non-negative integer of the right edge of the trimming range. If the reads are both forward and reverse 2 values should be given seperated with comma: 20,28
• --trunc: a non-negative integer of the left edge of the truncating range. If the reads are both forward and reverse 2 values should be given seperated with comma: 200,220
• --threads: Number of threads to run on. Default is 12. (Optional)

Note: All the parameters except --threads must be given.
Usage:

export-data --output-dir <output-directory-path> --trim <trim-from> --trunc <trunc-to> --threads <number-of-threads-to-use> --otu-output-file <otu-output-file-path> --taxonomy-output-file <taxonomy-output-file-path>