Metadata-Version: 2.1
Name: haystac
Version: 0.1
Summary: Species identification pipeline for both single species and metagenomic samples.
Home-page: https://github.com/antonisdim/haystac
Author: Evangelos A. Dimopoulos, Evan K. Irving-Pease
Author-email: antonisdim41@gmail.com
License: MIT
Description: HAYSTAC: High-AccuracY and Scalable Taxonomic Assignment of MetagenomiC data 
        ===
        
        Introduction 
        ------------
        
        Alignment based metagenomics
        ----------------------------
        
        `haystack` is an easy to use pipeline for metagenomic identifications 
        
        You can easily:
        
        1. Construct a database 
        2. Prepare your sample for analysis, including trimming sequencing adapters, collapsing paired end reads and also downloading data from the SRA
        3. Perform species identification 
        4. Perform a chemical damage pattern analysis 
        
        Setup 
        -----
        
        `haystac` can be run on any unix based system. It needs the conda package manager to run and it easy to install. 
        
        Quick Start 
        -----------
        
        Four commands/modules that allow you to run the method from start to finish 
        
        ```
        # install haystack from conda
        conda install -c bioconda haystac
        ```
        
        ```
        # build a target database of species you are interested in
        haystac database \
            --query '("Yersinia"[Organism] OR "Yersinia"[Organism]) AND "complete genome"[All Fields]' \
            --output yersinia_db
        ```
        
        ```
        # prepare a sample for analyis 
        haystac sample \
            --sra SRR12157896 \
            --collapse \
            --output SRR12157896
        ```
        
        ```
        # analyse a sample against a specific database
        haystac analyse \
            --mode abundances \
            --database yersinia_db \
            --sample SRR12157896 \
            --output yersinia_SRR12157896
        ```
        
        ```example commmands when I got them```
        
        
        License 
        -------
        
        MIT
        
        Citation 
        --------
        
        Happening soon 
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Description-Content-Type: text/markdown
