NCBI January, 2015 Hackathon - Metagenomics

Overview - Metagenomics pipeline for NCBI Hackathon

The following are a number of pipelines for viral discovery in whole (meta)genomic shotgun sequencing.

Description of the hackathon:

We assembled groups of genomics professionals to assess whether we could rapidly assemble pipelines to answer biological questions commonly asked by biologists and others new to bioinformatics. In January 2015, groups were assembled on the National Institutes of Health (NIH) campus to address questions in the DNA-seq, Epigenomics, Metagenomics and RNA-seq subfields of genomics. The only two rules set for this hackathon were that data either had to include those housed at the National Center for Biotechnology Information (NCBI) or from the participants (as long as they would be submitted to NCBI within six months of the hackathon), and that all software going into the pipeline had to be open-source or open-use. Proposed questions, as well as suggested tools and approaches, were distributed to participants a few days before the event and were refined during the event. Pipelines were published on Github, a web service providing publicly available, free-usage tiers for collaborative software development (https://github.com/features/). The code was published at https://github.com/DCGenomics/ with separate repositories for each team.

For more information on the goals of the hackathon, see:

PlosONE paper

Data Sources

To be filled in

NCBI's viral refseq

wget ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/*.fna*
gunzip *.fna*

Pipeline descriptions

To be filled in

Running the pipelines locally

NCBI's sratoolkit

wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.4.3/sratoolkit.2.4.3-ubuntu64.tar.gz
tar xfz sratoolkit.2.4.3-ubuntu64.tar.gz
export PATH=$PATH:$PWD/sratoolkit.2.4.3-ubuntu64/bin
vdb-config -i

‘latf-load’ , ‘blastn_vdb’, ‘fastq-dump’, ‘prefetch’, ‘vdb-config’, ‘align-info’, and ‘kar’ should now be in your path

Downloading the current pipelines

git clone https://github.com/DCGenomics/hackathon_v001_metagenomics.git
export PATH=$PATH:$PWD/hackathon_v001_metagenomics/sra_blast/bin/
export PATH=$PATH:$PWD/hackathon_v001_metagenomics/contig_blast/

Testing on two samples with sra_blast

sra_blast.sh -v /path/viral_refence.faa SRR00000 SRR00001
summarize_samples.R SRR00000.blast.results SRR00001.blast.results