haystac 0.1

Species identification pipeline for both single species and metagenomic samples.

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