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bfosso / MetaShot

MetaShot (Metagenomics Shotgun) is a complete pipeline designed for the taxonomic classification of the human microbiota members. In MetaShot, third party tools and new developed Python and Bash scripts are integrated to analyze paired-end (PE) Illumina sequences, offering an automated procedure covering all the analysis steps from raw data management to taxonomic profiling. It is designed to analyze both DNA-Seq and RNA-Seq data.
GNU General Public License v3.0
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MetaShot Application to Environmental Samples #2

Closed cam315 closed 5 years ago

cam315 commented 6 years ago

@bfosso As described in the Readme file, the tool package is designed for Human gut microbiome, I was wondering whether you have tested the pipeline with environmental samples? I would assume this is applicable, but need to use a more comprehensive reference database. Could you please give me some instruction in more detail? Thank you.

bfosso commented 6 years ago

Actually the MetaShot reference collection covers all the prokaryotes, viral and protist sequences available when I created them (about one years ago, the updating process is really slow and we are working on it). We tested the pipeline against a viral and bacterial mock communities and even if it works really well I think that you need to modify the Master script by commenting the host section.

cam315 commented 6 years ago

Thank you for your reply. For the modification you mentioned, could you please give me more instruction?

bfosso commented 6 years ago

I will prepare a Master script version for non human microbiome usage.

bfosso commented 5 years ago

I've added the -e option to the MetaShot_Master_script.py to exclude the comparison with the human genome. It is a simple walk around to avoid the STAR execution and maintain the general workflow.